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Conserved domains on  [gi|1958656771|ref|XP_038941247|]
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zinc phosphodiesterase ELAC protein 2 isoform X2 [Rattus norvegicus]

Protein Classification

MBL fold metallo-hydrolase( domain architecture ID 581040)

MBL fold metallo-hydrolase is most likely a hydrolytic enzyme

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 54-310 1.10e-102

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


The actual alignment was detected with superfamily member cd16296:

Pssm-ID: 451500 [Multi-domain]  Cd Length: 175  Bit Score: 301.88  E-value: 1.10e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  54 LQVVAAGGRDAGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCVLS 133
Cdd:cd16296     1 LQVVAAGSRDMGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLSGMILTLKETGLPKCVLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 134 GPpqlekyleaikifsgplkgidlavrphsapeykdetmtvyqvpihserrcgeqepsrspkrspnrlspkqsssdpgsa 213
Cdd:cd16296    81 GP------------------------------------------------------------------------------ 82

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 214 engqCLPEGSSAGVNGKAWGRDPSLVVAFVCKLHLRKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITYEGREIAAE 293
Cdd:cd16296    83 ----NKQSPDKIGVRRQILERDPSLVVAFICKLHLKKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITFEGREILAE 158

                         250
                  ....*....|....*..
gi 1958656771 294 ELCTPPDPGLVFIVVEC 310
Cdd:cd16296   159 ELCTPPDPGIVFIVVEC 175
 
Name Accession Description Interval E-value
RNaseZ_ELAC2-N-term-like_MBL-fold cd16296
Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase ...
 54-310 1.10e-102

Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. This eukaryotic subgroup includes the N-terminus of human ELAC2 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293854 [Multi-domain]  Cd Length: 175  Bit Score: 301.88  E-value: 1.10e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  54 LQVVAAGGRDAGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCVLS 133
Cdd:cd16296     1 LQVVAAGSRDMGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLSGMILTLKETGLPKCVLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 134 GPpqlekyleaikifsgplkgidlavrphsapeykdetmtvyqvpihserrcgeqepsrspkrspnrlspkqsssdpgsa 213
Cdd:cd16296    81 GP------------------------------------------------------------------------------ 82

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 214 engqCLPEGSSAGVNGKAWGRDPSLVVAFVCKLHLRKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITYEGREIAAE 293
Cdd:cd16296    83 ----NKQSPDKIGVRRQILERDPSLVVAFICKLHLKKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITFEGREILAE 158

                         250
                  ....*....|....*..
gi 1958656771 294 ELCTPPDPGLVFIVVEC 310
Cdd:cd16296   159 ELCTPPDPGIVFIVVEC 175
Lactamase_B_4 pfam13691
tRNase Z endonuclease; This is family of tRNase Z enzymes, that are closely related ...
 68-114 4.66e-15

tRNase Z endonuclease; This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localization signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues.


Pssm-ID: 404562 [Multi-domain]  Cd Length: 63  Bit Score: 69.15  E-value: 4.66e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958656771  68 LYVFSEYNRYLF-NCGEGVQRLMQEHKLKVARLDNIFLTRMH-WSNVGG 114
Cdd:pfam13691  15 LLLHFDSKRYLFgNVGEGTQRALNEQKVRLSKLEDIFLTGKVsWSNIGG 63
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
76-174 1.56e-13

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 69.84  E-value: 1.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  76 RYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPK-CVLSGPPQLEKYLEAIKIFSGPLKG 154
Cdd:COG1234    30 RLLIDCGEGTQRQLLRAGLDPRDIDAIFITHLHGDHIAGLPGLLSTRSLAGREKpLTIYGPPGTKEFLEALLKASGTDLD 109

                          90       100
                  ....*....|....*....|.
gi 1958656771 155 IDLAVRPHSAPE-YKDETMTV 174
Cdd:COG1234   110 FPLEFHEIEPGEvFEIGGFTV 130
PRK00055 PRK00055
ribonuclease Z; Reviewed
 77-152 1.03e-07

ribonuclease Z; Reviewed


Pssm-ID: 234602 [Multi-domain]  Cd Length: 270  Bit Score: 52.88  E-value: 1.03e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958656771  77 YLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCV-LSGPPQLEKYLEAIKIFSGPL 152
Cdd:PRK00055   32 FLFDCGEGTQRQLLKTGIKPRKIDKIFITHLHGDHIFGLPGLLSTRSLSGRTEPLtIYGPKGIKEFVETLLRASGSL 108
 
Name Accession Description Interval E-value
RNaseZ_ELAC2-N-term-like_MBL-fold cd16296
Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase ...
 54-310 1.10e-102

Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. This eukaryotic subgroup includes the N-terminus of human ELAC2 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293854 [Multi-domain]  Cd Length: 175  Bit Score: 301.88  E-value: 1.10e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  54 LQVVAAGGRDAGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCVLS 133
Cdd:cd16296     1 LQVVAAGSRDMGAALYVFSEYNRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLSGMILTLKETGLPKCVLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 134 GPpqlekyleaikifsgplkgidlavrphsapeykdetmtvyqvpihserrcgeqepsrspkrspnrlspkqsssdpgsa 213
Cdd:cd16296    81 GP------------------------------------------------------------------------------ 82

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771 214 engqCLPEGSSAGVNGKAWGRDPSLVVAFVCKLHLRKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITYEGREIAAE 293
Cdd:cd16296    83 ----NKQSPDKIGVRRQILERDPSLVVAFICKLHLKKGNFLVLKAKELGLPVGTAAIAPIIAAVKDGKSITFEGREILAE 158

                         250
                  ....*....|....*..
gi 1958656771 294 ELCTPPDPGLVFIVVEC 310
Cdd:cd16296   159 ELCTPPDPGIVFIVVEC 175
RNaseZ_MBL-fold cd16272
Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as ...
 75-166 9.28e-17

Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. It includes the C-terminus of human ELAC2 and Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293830 [Multi-domain]  Cd Length: 180  Bit Score: 77.69  E-value: 9.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  75 NRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPK-CVLSGPPQLEKYLEAIKIFSGPL- 152
Cdd:cd16272    27 TRILLDCGEGTVYRLLKAGVDPDKLDAIFLSHFHLDHIGGLPTLLFARRYGGRKKpLTIYGPKGIKEFLEKLLNFPVEIl 106

                          90
                  ....*....|....*
gi 1958656771 153 -KGIDLAVRPHSAPE 166
Cdd:cd16272   107 pLGFPLEIEELEEGG 121
Lactamase_B_4 pfam13691
tRNase Z endonuclease; This is family of tRNase Z enzymes, that are closely related ...
 68-114 4.66e-15

tRNase Z endonuclease; This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localization signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues.


Pssm-ID: 404562 [Multi-domain]  Cd Length: 63  Bit Score: 69.15  E-value: 4.66e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958656771  68 LYVFSEYNRYLF-NCGEGVQRLMQEHKLKVARLDNIFLTRMH-WSNVGG 114
Cdd:pfam13691  15 LLLHFDSKRYLFgNVGEGTQRALNEQKVRLSKLEDIFLTGKVsWSNIGG 63
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
76-174 1.56e-13

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 69.84  E-value: 1.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  76 RYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPK-CVLSGPPQLEKYLEAIKIFSGPLKG 154
Cdd:COG1234    30 RLLIDCGEGTQRQLLRAGLDPRDIDAIFITHLHGDHIAGLPGLLSTRSLAGREKpLTIYGPPGTKEFLEALLKASGTDLD 109

                          90       100
                  ....*....|....*....|.
gi 1958656771 155 IDLAVRPHSAPE-YKDETMTV 174
Cdd:COG1234   110 FPLEFHEIEPGEvFEIGGFTV 130
RNaseZ_ZiPD-like_MBL-fold cd07717
Ribonuclease Z, E. coli 3' tRNA-processing endonuclease ZiPD and related proteins; MBL-fold ...
 75-181 2.02e-13

Ribonuclease Z, E. coli 3' tRNA-processing endonuclease ZiPD and related proteins; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme; this subgroup includes the short form (ELAC1). Only the short form exists in bacteria. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293803 [Multi-domain]  Cd Length: 247  Bit Score: 69.40  E-value: 2.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656771  75 NRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHwsnvG----GLCGMILTLKETGLPKCV-LSGPPQLEKYLEAIKIFS 149
Cdd:cd07717    27 ELWLFDCGEGTQRQLLRAGLSPSKIDRIFITHLH----GdhilGLPGLLSTMSLLGRTEPLtIYGPKGLKEFLETLLRLS 102

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1958656771 150 GPLKGIDLAVRPHSAPE---YKDETMTVYQVPI-HS 181
Cdd:cd07717   103 ASRLPYPIEVHELEPDPglvFEDDGFTVTAFPLdHR 138
PRK00055 PRK00055
ribonuclease Z; Reviewed
 77-152 1.03e-07

ribonuclease Z; Reviewed


Pssm-ID: 234602 [Multi-domain]  Cd Length: 270  Bit Score: 52.88  E-value: 1.03e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958656771  77 YLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCV-LSGPPQLEKYLEAIKIFSGPL 152
Cdd:PRK00055   32 FLFDCGEGTQRQLLKTGIKPRKIDKIFITHLHGDHIFGLPGLLSTRSLSGRTEPLtIYGPKGIKEFVETLLRASGSL 108
arylsulfatase_AtsA-like_MBL-fold cd07719
Pseudoalteromonas carrageenovora arylsulfatase AtsA and related proteins; MBL-fold ...
 75-145 9.44e-04

Pseudoalteromonas carrageenovora arylsulfatase AtsA and related proteins; MBL-fold metallo-hydrolase domain; Arylsulfatase (also known as aryl-sulfate sulfohydrolase, EC 3.1.6.1). Pseudoalteromonas carrageenovora arylsulfatase AtsA may function as a glycosulfohydrolase involved with desulfation of sulfated polysaccharides, which catalyzes hydrolysis of the arylsulfate ester bond, producing the aryl compounds and inorganic sulfate. CD also includes some sequences annotated as ribonucleases. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily.


Pssm-ID: 293805 [Multi-domain]  Cd Length: 193  Bit Score: 40.19  E-value: 9.44e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958656771  75 NRYLFNCGEGVQRLMQEHKLKVARLDNIFLTRMHWSNVGGLCGMILTLKETGLPKCV-LSGPPQLEKYLEAI 145
Cdd:cd07719    28 RVYLVDAGSGVVRRLAQAGLPLGDLDAVFLTHLHSDHVADLPALLLTAWLAGRKTPLpVYGPPGTRALVDGL 99
 
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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