NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1176213384|gb|OQY24127|]
View 

hypothetical protein B6I35_02290 [Anaerolineaceae bacterium 4572_32.2]

Protein Classification

B12-binding domain-containing protein( domain architecture ID 11472039)

B12-binding domain-containing protein, similar to Methanosarcina barkeri methanol--corrinoid protein that acts as a methyl group carrier in methanogenesis in the methanol pathway

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MtbC1 COG5012
Methanogenic corrinoid protein MtbC1 [Energy production and conversion];
6-209 1.36e-59

Methanogenic corrinoid protein MtbC1 [Energy production and conversion];


:

Pssm-ID: 444036 [Multi-domain]  Cd Length: 219  Bit Score: 186.25  E-value: 1.36e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   6 DAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQElhgDAE 84
Cdd:COG5012    16 DAVLEGDEDEALELVAEALAAGMDPEEIILDGlAPGMREVGELWEEGEIFVPEEHLAAAAMKAGLEILKPLLAE---EGG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  85 AKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEA 164
Cdd:COG5012    93 RKGKVVIGTVEGDLHDIGKNIVADMLRAAGFEVIDLGADVPPEEFVEAAKEEKPDIVGLSALLTTTMPAMKELIEALREA 172

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1176213384 165 GLRESVKVIVGGGIVGEVKRTMLNVDHATTNANEGVRLIKRWITG 209
Cdd:COG5012   173 GLRDKVKVIVGGAPVTEELAEEIGADAYAEDAADAVELAKELLAE 217
 
Name Accession Description Interval E-value
MtbC1 COG5012
Methanogenic corrinoid protein MtbC1 [Energy production and conversion];
6-209 1.36e-59

Methanogenic corrinoid protein MtbC1 [Energy production and conversion];


Pssm-ID: 444036 [Multi-domain]  Cd Length: 219  Bit Score: 186.25  E-value: 1.36e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   6 DAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQElhgDAE 84
Cdd:COG5012    16 DAVLEGDEDEALELVAEALAAGMDPEEIILDGlAPGMREVGELWEEGEIFVPEEHLAAAAMKAGLEILKPLLAE---EGG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  85 AKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEA 164
Cdd:COG5012    93 RKGKVVIGTVEGDLHDIGKNIVADMLRAAGFEVIDLGADVPPEEFVEAAKEEKPDIVGLSALLTTTMPAMKELIEALREA 172

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1176213384 165 GLRESVKVIVGGGIVGEVKRTMLNVDHATTNANEGVRLIKRWITG 209
Cdd:COG5012   173 GLRDKVKVIVGGAPVTEELAEEIGADAYAEDAADAVELAKELLAE 217
corrinoid_protein_B12-BD cd02070
B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins ...
 4-204 3.21e-52

B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.


Pssm-ID: 239021 [Multi-domain]  Cd Length: 201  Bit Score: 166.64  E-value: 3.21e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   4 LGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQelHGD 82
Cdd:cd02070     1 LADAIVDGDEEETVELVKKALEAGIDPQDIIEEGlAPGMDIVGDKYEEGEIFVPELLMAADAMKAGLDLLKPLLG--KSK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  83 AEAKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIE 162
Cdd:cd02070    79 SAKKGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALK 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1176213384 163 EAGLRESVKVIVGGGIVGEVKRTMLNVDHATTNANEGVRLIK 204
Cdd:cd02070   159 EAGLRDKVKVMVGGAPVNQEFADEIGADGYAEDAAEAVAIAK 200
pyl_corrinoid TIGR02370
methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a ...
 3-198 5.15e-37

methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.


Pssm-ID: 131423 [Multi-domain]  Cd Length: 197  Bit Score: 127.61  E-value: 5.15e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   3 KLGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLqELHG 81
Cdd:TIGR02370   1 KLAKAIFEGEEDDVVEGAQKALDAGIDPIELIEKGlMAGMGVVGKLFEDGELFLPHVMMSADAMLAGIKVLTPEM-EKAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  82 DAEAKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAI 161
Cdd:TIGR02370  80 ETEVLGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDKL 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1176213384 162 EEAGLRESVKVIVGGGIVGEVKRTMLNVDHATTNANE 198
Cdd:TIGR02370 160 KEEGYRDSVKFMVGGAPVTQDWADKIGADVYGENASD 196
metH PRK09490
B12-dependent methionine synthase; Provisional
 30-148 5.75e-23

B12-dependent methionine synthase; Provisional


Pssm-ID: 236539 [Multi-domain]  Cd Length: 1229  Bit Score: 96.02  E-value: 5.75e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   30 PLEMVE----DarqGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQE---LHGDAEAKGVILMGTVAGDVHDLG 102
Cdd:PRK09490   691 PLEVIEgplmD---GMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEAkkeGGTDRKSNGKILMATVKGDVHDIG 767

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1176213384  103 KNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLT 148
Cdd:PRK09490   768 KNIVGVVLQCNNYEVIDLGVMVPAEKILETAKEENADIIGLSGLIT 813
B12-binding pfam02310
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
 87-179 6.27e-21

B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.


Pssm-ID: 426713 [Multi-domain]  Cd Length: 121  Bit Score: 83.91  E-value: 6.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  87 GVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIeeAGL 166
Cdd:pfam02310   1 GKVVVATVGGDLHPLGLNYVAAALRAAGFEVIILGANVPPEDIVAAARDEKPDVVGLSALMTTTLPGAKELIRLL--KGI 78

                          90
                  ....*....|...
gi 1176213384 167 RESVKVIVGGGIV 179
Cdd:pfam02310  79 RPRVKVVVGGPHP 91
B12-binding_2 smart01018
B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that ...
 3-78 1.83e-11

B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases.


Pssm-ID: 198086 [Multi-domain]  Cd Length: 84  Bit Score: 57.87  E-value: 1.83e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1176213384    3 KLGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQE 78
Cdd:smart01018   6 RLAEAIVDGDEEGVEELVEEALAEGVDPLEIINEGlIPGMNVVGDLFEAGEYFLPQVLMSAEAMKAAVAILKPLLEK 82
 
Name Accession Description Interval E-value
MtbC1 COG5012
Methanogenic corrinoid protein MtbC1 [Energy production and conversion];
6-209 1.36e-59

Methanogenic corrinoid protein MtbC1 [Energy production and conversion];


Pssm-ID: 444036 [Multi-domain]  Cd Length: 219  Bit Score: 186.25  E-value: 1.36e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   6 DAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQElhgDAE 84
Cdd:COG5012    16 DAVLEGDEDEALELVAEALAAGMDPEEIILDGlAPGMREVGELWEEGEIFVPEEHLAAAAMKAGLEILKPLLAE---EGG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  85 AKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEA 164
Cdd:COG5012    93 RKGKVVIGTVEGDLHDIGKNIVADMLRAAGFEVIDLGADVPPEEFVEAAKEEKPDIVGLSALLTTTMPAMKELIEALREA 172

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1176213384 165 GLRESVKVIVGGGIVGEVKRTMLNVDHATTNANEGVRLIKRWITG 209
Cdd:COG5012   173 GLRDKVKVIVGGAPVTEELAEEIGADAYAEDAADAVELAKELLAE 217
corrinoid_protein_B12-BD cd02070
B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins ...
 4-204 3.21e-52

B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.


Pssm-ID: 239021 [Multi-domain]  Cd Length: 201  Bit Score: 166.64  E-value: 3.21e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   4 LGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQelHGD 82
Cdd:cd02070     1 LADAIVDGDEEETVELVKKALEAGIDPQDIIEEGlAPGMDIVGDKYEEGEIFVPELLMAADAMKAGLDLLKPLLG--KSK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  83 AEAKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIE 162
Cdd:cd02070    79 SAKKGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALK 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1176213384 163 EAGLRESVKVIVGGGIVGEVKRTMLNVDHATTNANEGVRLIK 204
Cdd:cd02070   159 EAGLRDKVKVMVGGAPVNQEFADEIGADGYAEDAAEAVAIAK 200
MetH2 COG1410
Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; ...
 12-211 2.73e-43

Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Methionine synthase I, cobalamin-binding domain is part of the Pathway/BioSystem: Methionine biosynthesis


Pssm-ID: 441020 [Multi-domain]  Cd Length: 1141  Bit Score: 154.73  E-value: 2.73e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   12 DKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQELHGDAEAKGVIL 90
Cdd:COG1410    639 IKEGIEEDTEEALAEGARPLEIINGPlMPGMNVVGDLFGAGKMFLPQVLKSAEVMKAAVAYLEPFMEKEKGESSSKGKIV 718

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   91 MGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLResV 170
Cdd:COG1410    719 LATVKGDVHDIGKNIVGVVLENNGYEVIDLGVMVPAEKILEAAKEHKADIIGLSGLMTTSLDEMKEVAEEMRRRGLD--I 796

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1176213384  171 KVIVGGGIV----GEVK--RTMLNVDHATTNANEGVRLIKRWITGDQ 211
Cdd:COG1410    797 PVLIGGAALtrayTAVKiaPAYDGAVVYAKDASRAVRVADKLLSKER 843
pyl_corrinoid TIGR02370
methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a ...
 3-198 5.15e-37

methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.


Pssm-ID: 131423 [Multi-domain]  Cd Length: 197  Bit Score: 127.61  E-value: 5.15e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   3 KLGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLqELHG 81
Cdd:TIGR02370   1 KLAKAIFEGEEDDVVEGAQKALDAGIDPIELIEKGlMAGMGVVGKLFEDGELFLPHVMMSADAMLAGIKVLTPEM-EKAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  82 DAEAKGVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAI 161
Cdd:TIGR02370  80 ETEVLGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDKL 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1176213384 162 EEAGLRESVKVIVGGGIVGEVKRTMLNVDHATTNANE 198
Cdd:TIGR02370 160 KEEGYRDSVKFMVGGAPVTQDWADKIGADVYGENASD 196
methionine_synthase_B12_BD cd02069
B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as ...
 29-176 2.87e-29

B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).


Pssm-ID: 239020 [Multi-domain]  Cd Length: 213  Bit Score: 108.12  E-value: 2.87e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  29 DPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQELHGDAEAKGVILMGTVAGDVHDLGKNIVK 107
Cdd:cd02069    30 RPLEIINGPlMDGMKVVGDLFGAGKMFLPQVLKSARVMKAAVAYLEPYMEKEKGENSSKGKIVLATVKGDVHDIGKNLVG 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1176213384 108 DLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLreSVKVIVGG 176
Cdd:cd02069   110 VILSNNGYEVIDLGVMVPIEKILEAAKEHKADIIGLSGLLVPSLDEMVEVAEEMNRRGI--KIPLLIGG 176
metH TIGR02082
5-methyltetrahydrofolate--homocysteine methyltransferase; This family represents ...
 18-176 4.00e-27

5-methyltetrahydrofolate--homocysteine methyltransferase; This family represents 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13), one of at least three different enzymes able to convert homocysteine to methionine by transferring a methyl group on to the sulfur atom. It is also called the vitamin B12(or cobalamine)-dependent methionine synthase. Other methionine synthases include 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (MetE, EC 2.1.1.14, the cobalamin-independent methionine synthase) and betaine-homocysteine methyltransferase. [Amino acid biosynthesis, Aspartate family]


Pssm-ID: 273959 [Multi-domain]  Cd Length: 1181  Bit Score: 108.33  E-value: 4.00e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   18 AAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQELHGDAEAKGVILMGTVAG 96
Cdd:TIGR02082  664 EDLEEARKKLTRPLEIIEGPlMDGMKVVGDLFGSGKMFLPQVVKSARVMKKAVAYLEPHMEKEKSEDSSKGKIVLATVKG 743

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   97 DVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLResVKVIVGG 176
Cdd:TIGR02082  744 DVHDIGKNIVGVVLSCNGYEVVDLGVMVPIEKILEAAKDHNADVIGLSGLITPSLDEMKEVAEEMNRRGIT--IPLLIGG 821
B12-binding cd02067
B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 ...
 89-205 1.89e-26

B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.


Pssm-ID: 239018 [Multi-domain]  Cd Length: 119  Bit Score: 97.96  E-value: 1.89e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLrE 168
Cdd:cd02067     2 VVIATVGGDGHDIGKNIVARALRDAGFEVIDLGVDVPPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAGL-D 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1176213384 169 SVKVIVGGGIV--GEVKRTMLNVDHATTNANEGVRLIKR 205
Cdd:cd02067    81 DIPVLVGGAIVtrDFKFLKEIGVDAYFGPATEAVEVLKK 119
metH PRK09490
B12-dependent methionine synthase; Provisional
 30-148 5.75e-23

B12-dependent methionine synthase; Provisional


Pssm-ID: 236539 [Multi-domain]  Cd Length: 1229  Bit Score: 96.02  E-value: 5.75e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   30 PLEMVE----DarqGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQE---LHGDAEAKGVILMGTVAGDVHDLG 102
Cdd:PRK09490   691 PLEVIEgplmD---GMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEAkkeGGTDRKSNGKILMATVKGDVHDIG 767

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1176213384  103 KNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLT 148
Cdd:PRK09490   768 KNIVGVVLQCNNYEVIDLGVMVPAEKILETAKEENADIIGLSGLIT 813
B12-binding_like cd02065
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
 89-179 6.00e-21

B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.


Pssm-ID: 239016 [Multi-domain]  Cd Length: 125  Bit Score: 83.98  E-value: 6.00e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLRe 168
Cdd:cd02065     2 VLGATVGGDVHDIGKNIVAIALRDNGFEVIDLGVDVPPEEIVEAAKEEDADVVGLSALSTTHMEAMKLVIEALKELGID- 80

                          90
                  ....*....|.
gi 1176213384 169 sVKVIVGGGIV 179
Cdd:cd02065    81 -IPVVVGGAHP 90
B12-binding pfam02310
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
 87-179 6.27e-21

B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.


Pssm-ID: 426713 [Multi-domain]  Cd Length: 121  Bit Score: 83.91  E-value: 6.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  87 GVILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIeeAGL 166
Cdd:pfam02310   1 GKVVVATVGGDLHPLGLNYVAAALRAAGFEVIILGANVPPEDIVAAARDEKPDVVGLSALMTTTLPGAKELIRLL--KGI 78

                          90
                  ....*....|...
gi 1176213384 167 RESVKVIVGGGIV 179
Cdd:pfam02310  79 RPRVKVVVGGPHP 91
Sbm COG2185
Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid transport and ...
 89-185 1.77e-11

Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid transport and metabolism];


Pssm-ID: 441788 [Multi-domain]  Cd Length: 134  Bit Score: 59.39  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLRE 168
Cdd:COG2185    13 VLLAKPGLDGHDRGAKVIARALRDAGFEVIYLGLFQTPEEIVRAAIEEDADVIGVSSLDGGHLELVPELIELLKEAGAGD 92

                          90
                  ....*....|....*..
gi 1176213384 169 sVKVIVGGGIVGEVKRT 185
Cdd:COG2185    93 -ILVVVGGVIPPEDIEA 108
B12-binding_2 smart01018
B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that ...
 3-78 1.83e-11

B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases.


Pssm-ID: 198086 [Multi-domain]  Cd Length: 84  Bit Score: 57.87  E-value: 1.83e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1176213384    3 KLGDAMAALDKDIFLAAVKEGLTANQDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALIRPRLQE 78
Cdd:smart01018   6 RLAEAIVDGDEEGVEELVEEALAEGVDPLEIINEGlIPGMNVVGDLFEAGEYFLPQVLMSAEAMKAAVAILKPLLEK 82
MM_CoA_mut_B12_BD cd02071
methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), ...
 89-178 5.05e-06

methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.


Pssm-ID: 239022 [Multi-domain]  Cd Length: 122  Bit Score: 44.12  E-value: 5.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGlRE 168
Cdd:cd02071     2 ILVAKPGLDGHDRGAKVIARALRDAGFEVIYTGLRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELG-AG 80

                          90
                  ....*....|
gi 1176213384 169 SVKVIVGGGI 178
Cdd:cd02071    81 DILVVGGGII 90
PRK02261 PRK02261
methylaspartate mutase subunit S; Provisional
 89-179 5.14e-06

methylaspartate mutase subunit S; Provisional


Pssm-ID: 179400 [Multi-domain]  Cd Length: 137  Bit Score: 44.56  E-value: 5.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLRE 168
Cdd:PRK02261    6 VVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAAIETDADAILVSSLYGHGEIDCRGLREKCIEAGLGD 85

                          90
                  ....*....|.
gi 1176213384 169 sVKVIVGGGIV 179
Cdd:PRK02261   86 -ILLYVGGNLV 95
Glm_B12_BD cd02072
B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S) ...
 89-179 2.01e-05

B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.


Pssm-ID: 239023 [Multi-domain]  Cd Length: 128  Bit Score: 42.45  E-value: 2.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384  89 ILMGTVAGDVHDLGKNIVKDLLDCSGFEVIDLGVDVSTAKFIENIKEHHPQVVGMSALLTAAIGEVNKTVTAIEEAGLrE 168
Cdd:cd02072     2 IVLGVIGSDCHAVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAAIETDADAILVSSLYGHGEIDCKGLREKCDEAGL-K 80

                          90
                  ....*....|.
gi 1176213384 169 SVKVIVGGGIV 179
Cdd:cd02072    81 DILLYVGGNLV 91
B12-binding_2 pfam02607
B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and ...
 4-72 7.30e-05

B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.


Pssm-ID: 460617 [Multi-domain]  Cd Length: 68  Bit Score: 39.76  E-value: 7.30e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176213384   4 LGDAMAALDKDIFLAAVKEGLTAnqDPLEMVEDA-RQGLELVGAEFDQGNYFLMELMWAAEIFKDGMALI 72
Cdd:pfam02607   1 LLEALLEGDEEAAEELLEEALEI--DPEEIIEDLlIPGMDEVGELWEAGEIFVPQEHLAAEAMKAALAVL 68
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH