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Conserved domains on  [gi|15833132|ref|NP_311905|]
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maturation protease for hydrogenase 2 [Escherichia coli O157:H7 str. Sakai]

Protein Classification

HyaD/HybD family hydrogenase maturation endopeptidase( domain architecture ID 10793400)

HyaD/HybD family hydrogenase maturation endopeptidase similar to Escherichia coli hydrogenase 2 maturation protease which is involved in the C-terminal processing of HybC, the large subunit of hydrogenase 2, and specifically cleaves off a 15 amino acid peptide from the C-terminus of the precursor of HybC

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
hybD PRK10466
HyaD/HybD family hydrogenase maturation endopeptidase;
1-164 1.25e-104

HyaD/HybD family hydrogenase maturation endopeptidase;


:

Pssm-ID: 182481  Cd Length: 164  Bit Score: 296.22  E-value: 1.25e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKSAPGTMMILRDE 80
Cdd:PRK10466   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTIMVLRDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160
Cdd:PRK10466  81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160


                 ....
gi 15833132  161 AIHD 164
Cdd:PRK10466 161 AIHD 164
 
Name Accession Description Interval E-value
hybD PRK10466
HyaD/HybD family hydrogenase maturation endopeptidase;
1-164 1.25e-104

HyaD/HybD family hydrogenase maturation endopeptidase;


Pssm-ID: 182481  Cd Length: 164  Bit Score: 296.22  E-value: 1.25e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKSAPGTMMILRDE 80
Cdd:PRK10466   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTIMVLRDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160
Cdd:PRK10466  81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160


                 ....
gi 15833132  161 AIHD 164
Cdd:PRK10466 161 AIHD 164
H2MP_MemB-H2up cd06062
Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer ...
 3-149 5.29e-62

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: 187.66  E-value: 5.29e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   3 ILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAiVSKKSAPGTMMILRDEEV 82
Cdd:cd06062   1 ILVLGIGNILLADEGIGVHAVERLEENYSFPENVELIDGGTLGLELLPYIEEADRLIIVDA-VDAGGPPGTVYRFEGEDV 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15833132  83 PALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAAL 149
Cdd:cd06062  80 PAFLSAKLSAHQVGLLEVLALAELLGDLPPEIVLIGVQPESIEWGLELSPEVAAALPTAIEAVLAEL 146
hupD TIGR00140
hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are ...
 20-153 6.79e-59

hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease. [Protein fate, Protein modification and repair]


Pssm-ID: 129246  Cd Length: 134  Bit Score: 179.42  E-value: 6.79e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    20 VRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVPALFTNKISPHQLGLAD 99
Cdd:TIGR00140   1 VRLVEALQQRYAFPDNVTLLDGGTQGLYLLPLIESADRLIILDAVDYGL-EPGTLYILRDEEVPKFLAKKMSLHQTGFQE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15833132   100 VLSALRFTGEFPKKLTLVGVIPESLEPHIG-LTPTVEAMIEPALEQVLAALRESG 153
Cdd:TIGR00140  80 VLALAELLGHLPKELVLIGVQPEELEDYGGsLSPEVAEAIPPAIEIALAQLAEWG 134
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
1-151 1.03e-53

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


Pssm-ID: 440444  Cd Length: 150  Bit Score: 166.90  E-value: 1.03e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   1 MRILVLGVGNILLTDEAIGVRIVEALEQRyILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKkSAPGTMMILRDE 80
Cdd:COG0680   2 MKILVLGIGNPLRGDDGVGVRVAEALEER-ELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSG-AEPGTVRRLEPE 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833132  81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRE 151
Cdd:COG0680  80 ELPAGDASKLSTHQLGLAELLALARLLGDLPEEVVLIGIEPESLEFGEGLSPEVAAAVPKAVELILEELAE 150
HycI pfam01750
Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. ...
 20-148 2.37e-40

Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.


Pssm-ID: 396353  Cd Length: 130  Bit Score: 132.40  E-value: 2.37e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    20 VRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVPALFTNK-ISPHQLGLA 98
Cdd:pfam01750   1 VRVVEELKRRYAFPENVTVIDGGTGGLYLVGYLEEYDKLIIVDAVDFGL-EPGTVRIIDVDEVPKFLIAKkMSAHQLPLS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15833132    99 DVLSALRFTGEFPKKLTLVGVIPESLEP-HIGLTPTVEAMIEPALEQVLAA 148
Cdd:pfam01750  80 EVLRLLEELGEIPKVVILCGVQPVILEDyGGGLSEEVKKAIPRAVELILSE 130
 
Name Accession Description Interval E-value
hybD PRK10466
HyaD/HybD family hydrogenase maturation endopeptidase;
1-164 1.25e-104

HyaD/HybD family hydrogenase maturation endopeptidase;


Pssm-ID: 182481  Cd Length: 164  Bit Score: 296.22  E-value: 1.25e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKSAPGTMMILRDE 80
Cdd:PRK10466   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTIMVLRDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160
Cdd:PRK10466  81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRE 160


                 ....
gi 15833132  161 AIHD 164
Cdd:PRK10466 161 AIHD 164
H2MP_MemB-H2up cd06062
Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer ...
 3-149 5.29e-62

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: 187.66  E-value: 5.29e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   3 ILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAiVSKKSAPGTMMILRDEEV 82
Cdd:cd06062   1 ILVLGIGNILLADEGIGVHAVERLEENYSFPENVELIDGGTLGLELLPYIEEADRLIIVDA-VDAGGPPGTVYRFEGEDV 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15833132  83 PALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAAL 149
Cdd:cd06062  80 PAFLSAKLSAHQVGLLEVLALAELLGDLPPEIVLIGVQPESIEWGLELSPEVAAALPTAIEAVLAEL 146
hupD TIGR00140
hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are ...
 20-153 6.79e-59

hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease. [Protein fate, Protein modification and repair]


Pssm-ID: 129246  Cd Length: 134  Bit Score: 179.42  E-value: 6.79e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    20 VRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVPALFTNKISPHQLGLAD 99
Cdd:TIGR00140   1 VRLVEALQQRYAFPDNVTLLDGGTQGLYLLPLIESADRLIILDAVDYGL-EPGTLYILRDEEVPKFLAKKMSLHQTGFQE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15833132   100 VLSALRFTGEFPKKLTLVGVIPESLEPHIG-LTPTVEAMIEPALEQVLAALRESG 153
Cdd:TIGR00140  80 VLALAELLGHLPKELVLIGVQPEELEDYGGsLSPEVAEAIPPAIEIALAQLAEWG 134
hydrog_prot TIGR00072
hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for ...
 4-149 6.69e-56

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: 172.31  E-value: 6.69e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132     4 LVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVP 83
Cdd:TIGR00072   1 LVLGIGNILRGDDGFGPRVAERLEERYEFPPGVEVLDGGTLGLELLDALEGADRVIVVDAVDSGA-EPGTVRRLDGEDLP 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15833132    84 ALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAAL 149
Cdd:TIGR00072  80 AGLGGKLSTHQLGLAEALALLELLGALPPEIVLLGIQPESLEFGLGLSPEVAAAVPAAVELILAEL 145
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
1-151 1.03e-53

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


Pssm-ID: 440444  Cd Length: 150  Bit Score: 166.90  E-value: 1.03e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   1 MRILVLGVGNILLTDEAIGVRIVEALEQRyILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKkSAPGTMMILRDE 80
Cdd:COG0680   2 MKILVLGIGNPLRGDDGVGVRVAEALEER-ELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSG-AEPGTVRRLEPE 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833132  81 EVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRE 151
Cdd:COG0680  80 ELPAGDASKLSTHQLGLAELLALARLLGDLPEEVVLIGIEPESLEFGEGLSPEVAAAVPKAVELILEELAE 150
H2MP cd00518
Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases ...
 4-145 3.32e-44

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: 142.30  E-value: 3.32e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRYILPDyVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVP 83
Cdd:cd00518   1 LVLGIGNPLRGDDGFGPAVAERLEERYLPPG-VEVIDGGTLGLELLDLLEGADRVIIVDAVDSGG-EPGTVRRLEPEELP 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15833132  84 ALFTNkISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQV 145
Cdd:cd00518  79 AYLSA-LSTHQLGLAELLALLRLLGGLPPEVVLIGIQPESLELGEGLSPEVAAAVPKAVELI 139
HycI pfam01750
Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. ...
 20-148 2.37e-40

Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.


Pssm-ID: 396353  Cd Length: 130  Bit Score: 132.40  E-value: 2.37e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    20 VRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKsAPGTMMILRDEEVPALFTNK-ISPHQLGLA 98
Cdd:pfam01750   1 VRVVEELKRRYAFPENVTVIDGGTGGLYLVGYLEEYDKLIIVDAVDFGL-EPGTVRIIDVDEVPKFLIAKkMSAHQLPLS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15833132    99 DVLSALRFTGEFPKKLTLVGVIPESLEP-HIGLTPTVEAMIEPALEQVLAA 148
Cdd:pfam01750  80 EVLRLLEELGEIPKVVILCGVQPVILEDyGGGLSEEVKKAIPRAVELILSE 130
PRK10264 PRK10264
hydrogenase 1 maturation protease; Provisional
 2-160 6.58e-30

hydrogenase 1 maturation protease; Provisional


Pssm-ID: 182345  Cd Length: 195  Bit Score: 107.79  E-value: 6.58e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132    2 RILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIvSKKSAPGTMMILRDEE 81
Cdd:PRK10264   5 RVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAI-DYGLEPGTLRTYAGER 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   82 VPA-LFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQ-VLAALRESGVEAIPR 159
Cdd:PRK10264  84 IPAyLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQaALAQLAAWGIVPQPA 163


                 .
gi 15833132  160 E 160
Cdd:PRK10264 164 N 164
H2MP_Cyano-H2up cd06063
This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial ...
 5-151 5.67e-22

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: 85.91  E-value: 5.67e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   5 VLGVGNILLTDEAIGVRIVEALeQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAiVSKKSAPGTMMILRDEEVPA 84
Cdd:cd06063   3 IIGCGNLNRGDDGVGPILIRRL-QAYLLPPHVRLVDCGTAGMEVMFRARGAKQLIIIDA-SSTGSEPGAVFEVPGEELEA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15833132  85 LFTNKISPHQLGLADVLSALR--FTGEFPKKLTLVGVIPESLEPHIGLTPTVEAmiepALEQVLAALRE 151
Cdd:cd06063  81 LPEPSYNLHDFRWDHALAAGRkiFGDDFPKDVTVYLIEAKSLDFGLELSPPVKQ----AAERVAEMIIK 145
H2MP_F420-Reduc cd06064
Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from ...
 4-146 1.74e-18

Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D.


Pssm-ID: 99875  Cd Length: 150  Bit Score: 76.90  E-value: 1.74e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRD----HLIIADAIVSKKSaPGTMMILRD 79
Cdd:cd06064   1 LVVGCGNILFGDDGFGPAVIEELEKLELLPDNVQVIDAGTGAPHLLFTLLDEEskpkKIIIVDAIDFGLE-PGTLKKISV 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132  80 EEVPALFTNKISPHQLGLADVLsaLRFTGEFPKKLTLVGVIPESL-EPHI--GLTPTVEAMIEPALEQVL 146
Cdd:cd06064  80 DELPPGKYYDFDAHSWPLADPL--HELKDKYGIEIVVIGCQPKRVpEPDVepGLSEEVEKAVPKAVEIIL 147
H2MP_like-2 cd06070
Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity ...
 4-145 8.77e-18

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: 99879  Cd Length: 140  Bit Score: 74.77  E-value: 8.77e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRyilpdYVEILDGGTAGMELLGDMANRDHLIIADaIVSKKSAPGTMMI-LRDEEV 82
Cdd:cd06070   1 LIIGVGNRLYGDDGFGSCLAEALEQC-----GAPVFDGGLDGFGLLSHLENYDIVIFID-VAVIDEDVGVFKItPEPASV 74

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15833132  83 PALFTNKISPHQLGLADVLSALRFTGeFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQV 145
Cdd:cd06070  75 AEQISFETDAHRLGPAHLLLLLKSSG-RRPKAYIVGVKPESIEFARGLSEAVIARAEKALEEL 136
H2MP_like-1 cd06068
Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity ...
 4-145 5.99e-17

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: 72.75  E-value: 5.99e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRyILPDYVEILDGGTAGMELLGD-MANRDHLIIADAiVSKKSAPGTMMILRDEEV 82
Cdd:cd06068   1 LVAGVGNIFLGDDGFGVEVARRLRPR-QLPPGVRVADFGIRGIHLAYElLDGYDTLILVDA-VPRGGEPGTLYVIELEDV 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15833132  83 PALfTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQV 145
Cdd:cd06068  79 DAA-PELLDAHGMNPDAVLALLRALGGTPPRVVVVGCEPADVDEGIGLSEPVAAAVPEAVRLV 140
H2MP_MemB-H2evol cd06067
Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase ...
 4-134 8.96e-10

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: 53.71  E-value: 8.96e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRYIlpDYVEILDGGTAGMELLGDMANR--DHLIIADAiVSKKSAPGTMMILRDEE 81
Cdd:cd06067   1 VLLGVGNELRGDDGAGPLLAEKLEDLPN--PNWLVIDGGTVPENFTGKIREEkpDLIVIVDA-ADMGLEPGEIRIIDPEE 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 15833132  82 VPALFtnkISPHQLGLADVLSALR-FTGEfpkKLTLVGVIPESLEPHIGLTPTV 134
Cdd:cd06067  78 IAEYF---FSTHTLPLSILIDYLReSTGA---EVIFLGIQPENLEFGEPLSPEV 125
H2MP_NAD-link-bidir cd06066
Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of ...
 4-145 1.60e-06

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: 44.89  E-value: 1.60e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833132   4 LVLGVGNILLTDEAIGVRIVEALEQRyILPDyVEILDGGTAGMELLGDMANRDHLIIADAIVSKKSAPGTMmilrdEEVP 83
Cdd:cd06066   1 LVIGYGNPLRGDDGLGPAVAERIEEW-LLPG-VEVLAVHQLTPELAEDLAGADRVIFIDASLGGSPAPFRI-----VRLE 73

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15833132  84 ALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQV 145
Cdd:cd06066  74 PRRDSSFTSHALSPAALLALAQALYGHAPPAWLLTIPGYNFELGEPLSPAAEAALAAALELL 135
 
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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