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Conserved domains on  [gi|1221436501|ref|WP_089610649|]
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hydrogenase maturation protease [Dehalobacterium formicoaceticum]

Protein Classification

hydrogenase maturation protease( domain architecture ID 10087736)

hydrogenase maturation protease similar to Thermococcus kodakarensis [NiFe] hydrogenase maturation protease HybD, which is involved in the cleavage of the C-terminal residues of [NiFe] hydrogenase large subunits by Ni recognition

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
1-146 4.88e-25

Ni,Fe-hydrogenase maturation factor [Energy production and conversion];


:

Pssm-ID: 440444  Cd Length: 150  Bit Score: 93.71  E-value: 4.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   1 MIKVIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCEL 80
Cdd:COG0680     3 KILVLGIGNPLRGDDGVGVRVAE----ALEERELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSGAEPGTVRRLEP 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  81 QKAITAYGQTNSQHDMSVFDLMRLYSK----PVKGCFIGIEIAEAGFGCELSDALKDKFNDICLDVERII 146
Cdd:COG0680    79 EELPAGDASKLSTHQLGLAELLALARLlgdlPEEVVLIGIEPESLEFGEGLSPEVAAAVPKAVELILEEL 148
 
Name Accession Description Interval E-value
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
1-146 4.88e-25

Ni,Fe-hydrogenase maturation factor [Energy production and conversion];


Pssm-ID: 440444  Cd Length: 150  Bit Score: 93.71  E-value: 4.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   1 MIKVIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCEL 80
Cdd:COG0680     3 KILVLGIGNPLRGDDGVGVRVAE----ALEERELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSGAEPGTVRRLEP 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  81 QKAITAYGQTNSQHDMSVFDLMRLYSK----PVKGCFIGIEIAEAGFGCELSDALKDKFNDICLDVERII 146
Cdd:COG0680    79 EELPAGDASKLSTHQLGLAELLALARLlgdlPEEVVLIGIEPESLEFGEGLSPEVAAAVPKAVELILEEL 148
H2MP cd00518
Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases ...
 4-139 1.25e-22

Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.


Pssm-ID: 99872 [Multi-domain]  Cd Length: 139  Bit Score: 87.22  E-value: 1.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCELQkA 83
Cdd:cd00518     2 VLGIGNPLRGDDGFGPAVAE----RLEERYLPPGVEVIDGGTLGLELLDLLEGADRVIIVDAVDSGGEPGTVRRLEPE-E 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  84 ITAYGQTNSQHDMSVFDLMRL----YSKPVKGCFIGIEIAEAGFGCELSDALKDKFNDIC 139
Cdd:cd00518    77 LPAYLSALSTHQLGLAELLALlrllGGLPPEVVLIGIQPESLELGEGLSPEVAAAVPKAV 136
hydrog_prot TIGR00072
hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for ...
 4-132 2.86e-19

hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.


Pssm-ID: 272890  Cd Length: 145  Bit Score: 78.71  E-value: 2.86e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLENIRNKLAsigESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCELQKA 83
Cdd:TIGR00072   2 VLGIGNILRGDDGFGPRVAERLEERYE---FPPGVEVLDGGTLGLELLDALEGADRVIVVDAVDSGAEPGTVRRLDGEDL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1221436501  84 ITAYGQTNSQHDMSVFDLMRLYSK----PVKGCFIGIEIAEAGFGCELSDALK 132
Cdd:TIGR00072  79 PAGLGGKLSTHQLGLAEALALLELlgalPPEIVLLGIQPESLEFGLGLSPEVA 131
 
Name Accession Description Interval E-value
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
1-146 4.88e-25

Ni,Fe-hydrogenase maturation factor [Energy production and conversion];


Pssm-ID: 440444  Cd Length: 150  Bit Score: 93.71  E-value: 4.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   1 MIKVIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCEL 80
Cdd:COG0680     3 KILVLGIGNPLRGDDGVGVRVAE----ALEERELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSGAEPGTVRRLEP 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  81 QKAITAYGQTNSQHDMSVFDLMRLYSK----PVKGCFIGIEIAEAGFGCELSDALKDKFNDICLDVERII 146
Cdd:COG0680    79 EELPAGDASKLSTHQLGLAELLALARLlgdlPEEVVLIGIEPESLEFGEGLSPEVAAAVPKAVELILEEL 148
H2MP cd00518
Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases ...
 4-139 1.25e-22

Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.


Pssm-ID: 99872 [Multi-domain]  Cd Length: 139  Bit Score: 87.22  E-value: 1.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCELQkA 83
Cdd:cd00518     2 VLGIGNPLRGDDGFGPAVAE----RLEERYLPPGVEVIDGGTLGLELLDLLEGADRVIIVDAVDSGGEPGTVRRLEPE-E 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  84 ITAYGQTNSQHDMSVFDLMRL----YSKPVKGCFIGIEIAEAGFGCELSDALKDKFNDIC 139
Cdd:cd00518    77 LPAYLSALSTHQLGLAELLALlrllGGLPPEVVLIGIQPESLELGEGLSPEVAAAVPKAV 136
hydrog_prot TIGR00072
hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for ...
 4-132 2.86e-19

hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.


Pssm-ID: 272890  Cd Length: 145  Bit Score: 78.71  E-value: 2.86e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLENIRNKLAsigESVGIEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCELQKA 83
Cdd:TIGR00072   2 VLGIGNILRGDDGFGPRVAERLEERYE---FPPGVEVLDGGTLGLELLDALEGADRVIVVDAVDSGAEPGTVRRLDGEDL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1221436501  84 ITAYGQTNSQHDMSVFDLMRLYSK----PVKGCFIGIEIAEAGFGCELSDALK 132
Cdd:TIGR00072  79 PAGLGGKLSTHQLGLAEALALLELlgalPPEIVLLGIQPESLEFGLGLSPEVA 131
H2MP_MemB-H2up cd06062
Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer ...
 2-146 9.91e-11

Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.


Pssm-ID: 99873  Cd Length: 146  Bit Score: 56.31  E-value: 9.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   2 IKVIGIGNRLMMDDGIAIAVLENIRnKLASIGESVgiEVIIAETDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCELQ 81
Cdd:cd06062     1 ILVLGIGNILLADEGIGVHAVERLE-ENYSFPENV--ELIDGGTLGLELLPYIEEADRLIIVDAVDAGGPPGTVYRFEGE 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1221436501  82 KAITAYGQTNSQHDMSVFDLMRL----YSKPVKGCFIGIEIAEAGFGCELSDALKDKFNDICLDVERII 146
Cdd:cd06062    78 DVPAFLSAKLSAHQVGLLEVLALaellGDLPPEIVLIGVQPESIEWGLELSPEVAAALPTAIEAVLAEL 146
H2MP_MemB-H2evol cd06067
Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase ...
 4-138 2.82e-05

Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In the absence of this C-terminal stretch, there is no homolog of endopeptidase HycI found in these two related hydrogenase.


Pssm-ID: 99877  Cd Length: 136  Bit Score: 41.38  E-value: 2.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLENIRNKLAsigesVGIEVIIAETDFQFCFHQLRAD--DFVIVVDASYLGGGAGNVHSCELQ 81
Cdd:cd06067     2 LLGVGNELRGDDGAGPLLAEKLEDLPN-----PNWLVIDGGTVPENFTGKIREEkpDLIVIVDAADMGLEPGEIRIIDPE 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  82 KAITAYGQTnsqHDMS---VFDLMRLYSKPvKGCFIGIEIAEAGFGCELSDALKDKFNDI 138
Cdd:cd06067    77 EIAEYFFST---HTLPlsiLIDYLRESTGA-EVIFLGIQPENLEFGEPLSPEVKDAAEEL 132
H2MP_like-1 cd06068
Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity ...
 4-133 3.71e-05

Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.


Pssm-ID: 99878  Cd Length: 144  Bit Score: 41.17  E-value: 3.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLENIRNKLASIGESV---GIEviiaetDFQFCFHQLRADDFVIVVDASYLGGGAGNVHSCEL 80
Cdd:cd06068     2 VAGVGNIFLGDDGFGVEVARRLRPRQLPPGVRVadfGIR------GIHLAYELLDGYDTLILVDAVPRGGEPGTLYVIEL 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1221436501  81 QKaITAYGQTNSQHDMS---VFDLMR-LYSKPVKGCFIGIEIAEAGFGCELSDALKD 133
Cdd:cd06068    76 ED-VDAAPELLDAHGMNpdaVLALLRaLGGTPPRVVVVGCEPADVDEGIGLSEPVAA 131
H2MP_Cyano-H2up cd06063
This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial ...
 4-152 8.55e-05

This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus.


Pssm-ID: 99874  Cd Length: 146  Bit Score: 40.46  E-value: 8.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLEnirnKLASIGESVGIEVIIAETD-FQFCFHqLRADDFVIVVDASYLGGGAGNVHSCELQK 82
Cdd:cd06063     3 IIGCGNLNRGDDGVGPILIR----RLQAYLLPPHVRLVDCGTAgMEVMFR-ARGAKQLIIIDASSTGSEPGAVFEVPGEE 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221436501  83 AITAYGQTNSQHDMSVFDLMRLYSKPVKGCFIG------IEIAEAGFGCELSDALKDKfndicldVERIIFEIVKE 152
Cdd:cd06063    78 LEALPEPSYNLHDFRWDHALAAGRKIFGDDFPKdvtvylIEAKSLDFGLELSPPVKQA-------AERVAEMIIKE 146
H2MP_NAD-link-bidir cd06066
Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of ...
 4-131 8.82e-05

Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase.


Pssm-ID: 99876  Cd Length: 139  Bit Score: 40.27  E-value: 8.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501   4 VIGIGNRLMMDDGIAIAVLENIRNKLASigesvGIEVIIAetdfqfcfHQLRAD--------DFVIVVDASyLGGGAGNV 75
Cdd:cd06066     2 VIGYGNPLRGDDGLGPAVAERIEEWLLP-----GVEVLAV--------HQLTPElaedlagaDRVIFIDAS-LGGSPAPF 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221436501  76 HSCELQKAItayGQTNSQHDMSVFDLM----RLYSKPVKGCFIGIeiaeAGFGCELSDAL 131
Cdd:cd06066    68 RIVRLEPRR---DSSFTSHALSPAALLalaqALYGHAPPAWLLTI----PGYNFELGEPL 120
 
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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