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Conserved domains on  [gi|119593345|gb|EAW72939|]
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DPH5 homolog (S. cerevisiae), isoform CRA_f [Homo sapiens]

Protein Classification

SAM-dependent methyltransferase( domain architecture ID 148)

SAM-dependent methyltransferase catalyzes the methylation of one or more specific substrates using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor; belongs to the tetrapyrrole methylase family

CATH:  3.40.1010.10|3.30.950.10
EC:  2.1.1.-
Gene Ontology:  GO:1904047|GO:0008168
PubMed:  16225687
SCOP:  4000056

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
TP_methylase super family cl00304
S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet ...
 1-177 6.80e-115

S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide.


The actual alignment was detected with superfamily member PTZ00175:

Pssm-ID: 444820  Cd Length: 270  Bit Score: 326.92  E-value: 6.80e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVL-TVGKEALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:PTZ00175   2 MLYIIGLGLGDEKDITVKGLEAVKSADVVYLESYTSILiNSNKEKLEEFYGKPVIEADREMVEEGCDEILEEAKEKNVAF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMHT 159
Cdd:PTZ00175  82 LVVGDPFCATTHTDLYLRAKKKGIEVEVIHNASIMNAIGCTGLQLYRFGETVSIPFFTETWKPDSFYDKIKANRDNGLHT 161

                        170
                 ....*....|....*...
gi 119593345 160 LCLLDIKVKEQSLENLIK 177
Cdd:PTZ00175 162 LCLLDIKVKERSVENLMK 179
 
Name Accession Description Interval E-value
PTZ00175 PTZ00175
diphthine synthase; Provisional
 1-177 6.80e-115

diphthine synthase; Provisional


Pssm-ID: 185500  Cd Length: 270  Bit Score: 326.92  E-value: 6.80e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVL-TVGKEALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:PTZ00175   2 MLYIIGLGLGDEKDITVKGLEAVKSADVVYLESYTSILiNSNKEKLEEFYGKPVIEADREMVEEGCDEILEEAKEKNVAF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMHT 159
Cdd:PTZ00175  82 LVVGDPFCATTHTDLYLRAKKKGIEVEVIHNASIMNAIGCTGLQLYRFGETVSIPFFTETWKPDSFYDKIKANRDNGLHT 161

                        170
                 ....*....|....*...
gi 119593345 160 LCLLDIKVKEQSLENLIK 177
Cdd:PTZ00175 162 LCLLDIKVKERSVENLMK 179
DHP5_DphB cd11647
diphthine methyl ester synthase and diphthine synthase; Eukaryotic diphthine methyl ester ...
 1-169 3.54e-107

diphthine methyl ester synthase and diphthine synthase; Eukaryotic diphthine methyl ester synthase (DHP5) and archaeal diphthamide synthase (DphB) participate in the second step of the biosynthetic pathway of diphthamide. The eukaryotic enzyme catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester; the archaeal enzyme, catalyzes only 3 methylations, producing diphthine. Diphtheria toxin ADP-ribosylates diphthamide leading to inhibition of protein synthesis in the eukaryotic host cells.


Pssm-ID: 381174  Cd Length: 241  Bit Score: 306.27  E-value: 3.54e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLTVGK-EALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:cd11647    1 MLYLIGLGLGDEKDITLEGLEALKKADKVYLEAYTSILPGSKlEELEKLIGKKIILLDREDLEEESEEILEEAKKKDVAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCC-GLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:cd11647   81 LVPGDPLIATTHIDLRLEAKKRGIKVKVIHNASILSAAGSTsGLQLYKFGRTVTIPFPEENYKPESPYDVIKENLKRGLH 160

                        170
                 ....*....|.
gi 119593345 159 TLCLLDIKVKE 169
Cdd:cd11647  161 TLLLLDIKVEE 171
dph5 TIGR00522
diphthine synthase; Alternate name: diphthamide biosynthesis S-adenosylmethionine-dependent ...
 1-177 1.65e-79

diphthine synthase; Alternate name: diphthamide biosynthesis S-adenosylmethionine-dependent methyltransferase. This protein participates in the modification of a specific His of elongation factor 2 of eukarotes and Archaea to diphthamide. The protein was characterized in Saccharomyces cerevisiae and designated DPH5. [Protein fate, Protein modification and repair]


Pssm-ID: 273117  Cd Length: 257  Bit Score: 236.63  E-value: 1.65e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLTVGK-EALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:TIGR00522   1 MLYLIGLGLYDENDISVKGLEAIKKADEVYAEFYTSKLLGSSiEEIEEFFGKRVVVLERSDVEENSFRLIERAKSKDVAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAV-GCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:TIGR00522  81 LVAGDPMVATTHTDLKLEAKRKGIETRIIHGASISSAVcGLTGLQLYKFGKTATIVFFTDNYRPQTPYNVIKENRKIGLH 160

                         170       180
                  ....*....|....*....|....*.
gi 119593345  159 TLCLLDIKVKE-------QSLENLIK 177
Cdd:TIGR00522 161 TLVLLDIHPKEnramtigEGLENLLE 186
DPH5 COG1798
Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis];
1-170 2.40e-78

Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441403  Cd Length: 255  Bit Score: 233.55  E-value: 2.40e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLT-VGKEALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:COG1798    1 MLTFVGLGLSDERDITLKGLEALRSADKVYAEFYTSRLIgTDLEKLEELIGKEIVVLDREDVEDNPEEILEEAKEKDVVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAV-GCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:COG1798   81 LTAGDPMIATTHVDLRLRAKRRGIETRVIHGVSIVSAAiGLTGLQNYKFGKTVTIPFPYEGFVPTSPYDTIKENLERGLH 160

                        170
                 ....*....|..
gi 119593345 159 TLCLLDIKVKEQ 170
Cdd:COG1798  161 TLVLLDIKADKN 172
TP_methylase pfam00590
Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of ...
 1-177 1.12e-24

Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase.


Pssm-ID: 425769 [Multi-domain]  Cd Length: 209  Bit Score: 95.10  E-value: 1.12e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLE---AYTSVLTVGKEALeeFYGRKLVVADREEVEQEADNILKDA--DIS 75
Cdd:pfam00590   1 KLYLVGVGPGDPDLLTLRALRALKEADVVLGDdsrALEILLDLLPEDL--YFPMTEDKEPLEEAYEEIAEALAAAlrAGK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   76 DVAFLVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCC-GLQLYKFGETVSIVFWTDT-WRPESFFDKVKKNR 153
Cdd:pfam00590  79 DVARLVSGDPLVYGTGSYLVEALRAAGIDVEVVPGVSSAQAAAARlGIPLTEGGEVLSVLFLPGLaRIELRLLEALLANG 158

                         170       180
                  ....*....|....*....|....*
gi 119593345  154 qngmHTLCLLDIKVK-EQSLENLIK 177
Cdd:pfam00590 159 ----DTVVLLYGPRRlAELAELLLE 179
 
Name Accession Description Interval E-value
PTZ00175 PTZ00175
diphthine synthase; Provisional
 1-177 6.80e-115

diphthine synthase; Provisional


Pssm-ID: 185500  Cd Length: 270  Bit Score: 326.92  E-value: 6.80e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVL-TVGKEALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:PTZ00175   2 MLYIIGLGLGDEKDITVKGLEAVKSADVVYLESYTSILiNSNKEKLEEFYGKPVIEADREMVEEGCDEILEEAKEKNVAF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMHT 159
Cdd:PTZ00175  82 LVVGDPFCATTHTDLYLRAKKKGIEVEVIHNASIMNAIGCTGLQLYRFGETVSIPFFTETWKPDSFYDKIKANRDNGLHT 161

                        170
                 ....*....|....*...
gi 119593345 160 LCLLDIKVKEQSLENLIK 177
Cdd:PTZ00175 162 LCLLDIKVKERSVENLMK 179
DHP5_DphB cd11647
diphthine methyl ester synthase and diphthine synthase; Eukaryotic diphthine methyl ester ...
 1-169 3.54e-107

diphthine methyl ester synthase and diphthine synthase; Eukaryotic diphthine methyl ester synthase (DHP5) and archaeal diphthamide synthase (DphB) participate in the second step of the biosynthetic pathway of diphthamide. The eukaryotic enzyme catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester; the archaeal enzyme, catalyzes only 3 methylations, producing diphthine. Diphtheria toxin ADP-ribosylates diphthamide leading to inhibition of protein synthesis in the eukaryotic host cells.


Pssm-ID: 381174  Cd Length: 241  Bit Score: 306.27  E-value: 3.54e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLTVGK-EALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:cd11647    1 MLYLIGLGLGDEKDITLEGLEALKKADKVYLEAYTSILPGSKlEELEKLIGKKIILLDREDLEEESEEILEEAKKKDVAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCC-GLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:cd11647   81 LVPGDPLIATTHIDLRLEAKKRGIKVKVIHNASILSAAGSTsGLQLYKFGRTVTIPFPEENYKPESPYDVIKENLKRGLH 160

                        170
                 ....*....|.
gi 119593345 159 TLCLLDIKVKE 169
Cdd:cd11647  161 TLLLLDIKVEE 171
dph5 TIGR00522
diphthine synthase; Alternate name: diphthamide biosynthesis S-adenosylmethionine-dependent ...
 1-177 1.65e-79

diphthine synthase; Alternate name: diphthamide biosynthesis S-adenosylmethionine-dependent methyltransferase. This protein participates in the modification of a specific His of elongation factor 2 of eukarotes and Archaea to diphthamide. The protein was characterized in Saccharomyces cerevisiae and designated DPH5. [Protein fate, Protein modification and repair]


Pssm-ID: 273117  Cd Length: 257  Bit Score: 236.63  E-value: 1.65e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLTVGK-EALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:TIGR00522   1 MLYLIGLGLYDENDISVKGLEAIKKADEVYAEFYTSKLLGSSiEEIEEFFGKRVVVLERSDVEENSFRLIERAKSKDVAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAV-GCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:TIGR00522  81 LVAGDPMVATTHTDLKLEAKRKGIETRIIHGASISSAVcGLTGLQLYKFGKTATIVFFTDNYRPQTPYNVIKENRKIGLH 160

                         170       180
                  ....*....|....*....|....*.
gi 119593345  159 TLCLLDIKVKE-------QSLENLIK 177
Cdd:TIGR00522 161 TLVLLDIHPKEnramtigEGLENLLE 186
DPH5 COG1798
Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis];
1-170 2.40e-78

Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441403  Cd Length: 255  Bit Score: 233.55  E-value: 2.40e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLT-VGKEALEEFYGRKLVVADREEVEQEADNILKDADISDVAF 79
Cdd:COG1798    1 MLTFVGLGLSDERDITLKGLEALRSADKVYAEFYTSRLIgTDLEKLEELIGKEIVVLDREDVEDNPEEILEEAKEKDVVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  80 LVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAV-GCCGLQLYKFGETVSIVFWTDTWRPESFFDKVKKNRQNGMH 158
Cdd:COG1798   81 LTAGDPMIATTHVDLRLRAKRRGIETRVIHGVSIVSAAiGLTGLQNYKFGKTVTIPFPYEGFVPTSPYDTIKENLERGLH 160

                        170
                 ....*....|..
gi 119593345 159 TLCLLDIKVKEQ 170
Cdd:COG1798  161 TLVLLDIKADKN 172
TP_methylase pfam00590
Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of ...
 1-177 1.12e-24

Tetrapyrrole (Corrin/Porphyrin) Methylases; This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase.


Pssm-ID: 425769 [Multi-domain]  Cd Length: 209  Bit Score: 95.10  E-value: 1.12e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLE---AYTSVLTVGKEALeeFYGRKLVVADREEVEQEADNILKDA--DIS 75
Cdd:pfam00590   1 KLYLVGVGPGDPDLLTLRALRALKEADVVLGDdsrALEILLDLLPEDL--YFPMTEDKEPLEEAYEEIAEALAAAlrAGK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   76 DVAFLVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGCC-GLQLYKFGETVSIVFWTDT-WRPESFFDKVKKNR 153
Cdd:pfam00590  79 DVARLVSGDPLVYGTGSYLVEALRAAGIDVEVVPGVSSAQAAAARlGIPLTEGGEVLSVLFLPGLaRIELRLLEALLANG 158

                         170       180
                  ....*....|....*....|....*
gi 119593345  154 qngmHTLCLLDIKVK-EQSLENLIK 177
Cdd:pfam00590 159 ----DTVVLLYGPRRlAELAELLLE 179
TP_methylase cd09815
S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet ...
 5-177 9.91e-23

S-AdoMet-dependent tetrapyrrole methylases; This superfamily uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide.


Pssm-ID: 381167 [Multi-domain]  Cd Length: 219  Bit Score: 90.14  E-value: 9.91e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   5 IGLGLGDAKDITVKGLEVVRRCSRVYLEAYTSVLTVGKEALEEFYG-RKLVVADREEVEQEADNILKDADIS-DVAFLVV 82
Cdd:cd09815    1 VGVGPGDPDLLTLRALEILRAADVVVAEDKDSKLLSLVLRAILKDGkRIYDLHDPNVEEEMAELLLEEARQGkDVAFLSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345  83 GDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAVGC-CGLQLYKFGETVSIVFWTDTWRpesfFDKVKKNRQNGMHTLC 161
Cdd:cd09815   81 GDPGVAGTGAELVERAEREGVEVKVIPGVSAADAAAAaLGIDLGESFLFVTASDLLENPR----LLVLKALAKERRHLVL 156

                        170
                 ....*....|....*.
gi 119593345 162 LLDIKVKEQSLENLIK 177
Cdd:cd09815  157 FLDGHRFLKALERLLK 172
YabN_N_like cd11723
N-terminal S-AdoMet-dependent tetrapyrrole methylase domain of Bacillus subtilis YabN and ...
 2-124 2.93e-08

N-terminal S-AdoMet-dependent tetrapyrrole methylase domain of Bacillus subtilis YabN and similar domains; This family includes the S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent tetrapyrrole methylase (TP-methylase) domain of Bacillus subtilis YabN, and similar domains. YabN is a fusion of an N-terminal TP-methylase and a C-terminal MazG-type nucleotide pyrophosphohydrolase domain. MazG-like NTP-PPases have been implicated in house-cleaning functions such as degrading abnormal (d)NTPs. TP-methylases use S-AdoMet in the methylation of diverse substrates. Most TP-methylase family members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis, other members like diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) act on other substrates. The specific function of YabN's TP-methylase domain is not known.


Pssm-ID: 381177  Cd Length: 218  Bit Score: 51.33  E-value: 2.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   2 LYLIGLGLGDAKDITVKGLEVVRRCSRVYL-----EAYTSVLTVGK--EALEEFYGRKlvvADREEVEQE-ADNILKDAD 73
Cdd:cd11723    1 ITIVGLGPGDPDLLTLGALEALKSADKVYLrtarhPVVEELKEEGIefESFDDLYEEA---EDFEEVYEAiAERLLEAAE 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 119593345  74 ISDVAFLVVGDPFGATTHSDLVLRATKLGIPYRVIHNAS----IMNAVGCC---GLQL 124
Cdd:cd11723   78 HGDVVYAVPGHPLVAERTVQLLLERAEEGIEVEIIPGVSfldaALAALGIDpieGLQI 135
TP_methylase cd11724
uncharacterized family of the tetrapyrrole methylase superfamily; Members of this superfamily ...
 2-87 5.27e-08

uncharacterized family of the tetrapyrrole methylase superfamily; Members of this superfamily use S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and Ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide.


Pssm-ID: 381178 [Multi-domain]  Cd Length: 243  Bit Score: 50.63  E-value: 5.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   2 LYLIGLGLGDAKDITVKGLEVVRR-----CSRVYLEAYTSVLTvGKEALE------EFYGRKLVVADREEVEQEADNILK 70
Cdd:cd11724    2 LYLVGVGPGDPDLITLRALKAIKKadvvfAPPDLRKRFAEYLA-GKEVLDdphglfTYYGKKCSPLEEAEKECEELEKQR 80

                         90       100
                 ....*....|....*....|....*....
gi 119593345  71 DADIS----------DVAFLVVGDP--FG 87
Cdd:cd11724   81 AEIVQkirealaqgkNVALLDSGDPtiYG 109
PRK05576 PRK05576
cobalt-factor II C(20)-methyltransferase;
1-108 1.54e-07

cobalt-factor II C(20)-methyltransferase;


Pssm-ID: 235512 [Multi-domain]  Cd Length: 229  Bit Score: 49.53  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYleAYTSVLTVGKEAL---EEFYGRKLVV--------ADREEVEQE----A 65
Cdd:PRK05576   3 KLYGIGLGPGDPELLTVKAARILEEADVVY--APASRKGGGSLALnivRPYLKEETEIvelhfpmsKDEEEKEAVwkenA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 119593345  66 DNILKDA-DISDVAFLVVGDPFGATTHSDLVLRATKLGIPYRVI 108
Cdd:PRK05576  81 EEIAAEAeEGKNVAFITLGDPNLYSTFSHLLEYLKCHDIEVETV 124
CobF COG2243
Precorrin-2 methylase [Coenzyme transport and metabolism]; Precorrin-2 methylase is part of ...
 2-108 2.29e-07

Precorrin-2 methylase [Coenzyme transport and metabolism]; Precorrin-2 methylase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 441844 [Multi-domain]  Cd Length: 229  Bit Score: 48.94  E-value: 2.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   2 LYLIGLGLGDAKDITVKGLEVVRRCSRV-------------------YLEAYTSV-----LTVGKEALEEFYgrklvvad 57
Cdd:COG2243    5 LYGVGVGPGDPELLTLKAVRALREADVIaypakgagkaslareivapYLPPARIVelvfpMTTDYEALVAAW-------- 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119593345  58 reevEQEADNILKDADI-SDVAFLVVGDPF--GATTHsdLVLRATKLGIPYRVI 108
Cdd:COG2243   77 ----DEAAARIAEELEAgRDVAFLTEGDPSlySTFMY--LLERLRERGFEVEVI 124
cobI_cbiL TIGR01467
precorrin-2 C(20)-methyltransferase; This model represents precorrin-2 C(20)-methyltransferase, ...
 1-117 6.30e-06

precorrin-2 C(20)-methyltransferase; This model represents precorrin-2 C(20)-methyltransferase, one of several closely related S-adenosylmethionine-dependent methyltransferases involved in cobalamin (vitamin B12) biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 273642 [Multi-domain]  Cd Length: 230  Bit Score: 44.61  E-value: 6.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYLEAytsvltvgKEALEEFYGRKLV------------------VADREEVE 62
Cdd:TIGR01467   2 KLYGVGVGPGDPELITVKALEALRSADVIAVPA--------SKKGRESLARKIVedylkpndtrilelvfpmTKDRDELE 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   63 Q---EADNILKDA--DISDVAFLVVGDPFGATTHSDLVLRATKLGIPYRVIHNASIMNAV 117
Cdd:TIGR01467  74 KawdEAAEAVAAEleEGRDVAFLTLGDPSLYSTFSYLLQRLQGMGIEVEVVPGITSFAAC 133
PRK05787 PRK05787
cobalt-precorrin-7 (C(5))-methyltransferase;
1-85 5.13e-04

cobalt-precorrin-7 (C(5))-methyltransferase;


Pssm-ID: 235609 [Multi-domain]  Cd Length: 210  Bit Score: 39.08  E-value: 5.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   1 MLYLIGLGLGDAKDITVKGLEVVRRCSRVYleaytsvltVGKEALEEFygRKLVVADREEV----EQEADNILKDADISD 76
Cdd:PRK05787   1 MIYIVGIGPGDPEYLTLKALEAIRKADVVV---------GSKRVLELF--PELIDGEAFVLtaglRDLLEWLELAAKGKN 69


                 ....*....
gi 119593345  77 VAFLVVGDP 85
Cdd:PRK05787  70 VVVLSTGDP 78
Precorrin_2_C20_MT cd11645
Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Precorrin-2 C20-methyltransferase ...
 5-86 6.02e-04

Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Precorrin-2 C20-methyltransferase (also known as S-adenosyl-L-methionine--precorrin-2 methyltransferase) participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. Precorrin-2 C20-methyltransferase catalyzes methylation at the C-20 position of a cyclic tetrapyrrole ring of precorrin-2 using S-adenosylmethionine as a methyl group source to produce precorrin-3A. In the anaerobic pathway, cobalt is inserted into precorrin-2 by CbiK to generate cobalt-precorrin-2, which is the substrate for CbiL, a C20 methyltransferase. In Clostridium difficile, CbiK and CbiL are fused into a bifunctional enzyme. In the aerobic pathway, the precorrin-2 C20-methyltransferase is named CobI. This family includes CbiL and CobI precorrin-2 C20-methyltransferases, both as stand-alone enzymes and when CbiL forms part of a bifunctional enzyme.


Pssm-ID: 381172 [Multi-domain]  Cd Length: 223  Bit Score: 39.03  E-value: 6.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   5 IGLGLGDAKDITVKGLEVVRRCSRVYL---EAYTSVLTVGKEALEEFYGRKLV------VADREEVEQE----ADNILKD 71
Cdd:cd11645    1 VGVGPGDPELLTLKAVRILKEADVIFVpvsKGGEGSAALIIAAALLIPDKEIIplefpmTKDREELEEAwdeaAEEIAEE 80

                         90
                 ....*....|....*.
gi 119593345  72 ADIS-DVAFLVVGDPF 86
Cdd:cd11645   81 LKEGkDVAFLTLGDPS 96
cobM_cbiF TIGR01465
precorrin-4 C11-methyltransferase; This model represents precorrin-4 C11-methyltransferase, ...
 2-108 1.13e-03

precorrin-4 C11-methyltransferase; This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]


Pssm-ID: 200107  Cd Length: 247  Bit Score: 38.46  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345    2 LYLIGLGLGDAKDITVKGLEVVRRCSRVYleaYTSVLtVGKEALEEFYGRKLVVADREEVEQEADNILKDA--DISDVAF 79
Cdd:TIGR01465   1 VYFIGAGPGDPDLITVKGRKLIESADVIL---YAGSL-VPPELLAHCRPGAEVVNSAGMSLEEIVDIMSDAhrEGKDVAR 76

                          90       100       110
                  ....*....|....*....|....*....|.
gi 119593345   80 LVVGDP--FGATTHSDLVLRAtkLGIPYRVI 108
Cdd:TIGR01465  77 LHSGDPsiYGAIAEQMRLLEA--LGIPYEVV 105
PLN02625 PLN02625
uroporphyrin-III C-methyltransferase
 3-137 1.85e-03

uroporphyrin-III C-methyltransferase


Pssm-ID: 178232 [Multi-domain]  Cd Length: 263  Bit Score: 37.69  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   3 YLIGLGLGDAKDITVKGLEVVRRCSRVYLE--AYTSVLTVGKEALEEFYGRKLvvADREEVEQ-EADNILKD--ADISDV 77
Cdd:PLN02625  18 FLVGTGPGDPDLLTLKALRLLQTADVVLYDrlVSPDILDLVPPGAELLYVGKR--GGYHSRTQeEIHELLLSfaEAGKTV 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 119593345  78 AFLVVGDP--FGATTHSDLVLRatKLGIPYRVIhnASIMNAVGCC---GLQLYKFGETVSIVFWT 137
Cdd:PLN02625  96 VRLKGGDPlvFGRGGEEMDALR--KNGIPVTVV--PGITAAIGAPaelGIPLTHRGVATSVRFLT 156
Precorrin-4_C11-MT cd11641
Precorrin-4 C11-methyltransferase (CbiF/CobM); Precorrin-4 C11-methyltransferase participates ...
 5-108 2.54e-03

Precorrin-4 C11-methyltransferase (CbiF/CobM); Precorrin-4 C11-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. In the aerobic pathway, CobM catalyzes the methylation of precorrin-4 at C-11 to yield precorrin-5. In the anaerobic pathway, CibF catalyzes the methylation of cobalt-precorrin-4 to cobalt-precorrin-5. Both CibF and CobM, which are homologous, are included in this model. There are about 30 enzymes involved in vitamin B12 synthetic pathway. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared in both pathways and several of these enzymes are pathway-specific.


Pssm-ID: 381168 [Multi-domain]  Cd Length: 225  Bit Score: 36.99  E-value: 2.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   5 IGLGLGDAKDITVKGLEVVRRCSRVYleaYTSVLtVGKEALEEFYGRKLVVA----DREEVEQeadnILKDADIS--DVA 78
Cdd:cd11641    1 VGAGPGDPELITVKGARLLEEADVVI---YAGSL-VPPELLAYAKPGAEIVDsagmTLEEIIE----VMREAAREgkDVV 72

                         90       100       110
                 ....*....|....*....|....*....|..
gi 119593345  79 FLVVGDP--FGATTHSDLVLRatKLGIPYRVI 108
Cdd:cd11641   73 RLHTGDPslYGAIREQIDALD--KLGIPYEVV 102
Precorrin-6Y-MT cd11644
Precorrin-6Y methyltransferase (also named CbiE); CbiE (precorrin-6Y methyltransferase, also ...
 5-86 3.00e-03

Precorrin-6Y methyltransferase (also named CbiE); CbiE (precorrin-6Y methyltransferase, also known as cobalt-precorrin-7 C(5)-methyltransferase, also known as cobalt-precorrin-6Y C(5)-methyltransferase) catalyzes the methylation of C-5 in cobalt-precorrin-7 to form cobalt-precorrin-8. It participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. CbiE functions in the anaerobic pathway, it is a subunit of precorrin-6Y C5,15-methyltransferase, a bifunctional enzyme: cobalt-precorrin-7 C(5)-methyltransferase (CbiE)/cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) (CbiT), that catalyzes two methylations (at C-5 and C-15) in precorrin-6Y, as well as the decarboxylation of the acetate side chain located in ring C, in order to generate precorrin-8X. CbiE and CbiT can be found fused (CbiET, also called CobL), or on separate protein chains (CbiE and CbiT). In the aerobic pathway, a single enzyme called CobL catalyzes the methylations at C-5 and C-15, and the decarboxylation of the C-12 acetate side chain of precorrin-6B.


Pssm-ID: 381171 [Multi-domain]  Cd Length: 198  Bit Score: 36.70  E-value: 3.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119593345   5 IGLGLGDAKDITVKGLEVVRRCSRVYleAYTSVLtvgkEALEEFYGRKLVVAdREEVEQEADNILKDADisDVAFLVVGD 84
Cdd:cd11644    1 IGIGPGGPEYLTPEAREAIEEADVVI--GAKRLL----ELFPDLGAEKIPLP-SEDIAELLEEIAEAGK--RVVVLASGD 71


                 ..
gi 119593345  85 PF 86
Cdd:cd11644   72 PG 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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