Conserved Protein Domain Family
H2MP

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cd00518: H2MP 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 99872
View PSSM: cd00518
Aligned: 198 rows
Threshold Bit Score: 66.03
Threshold Setting Gi: 160353485
Created: 7-Mar-2002
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
nickel binding
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:nickel binding site [ion binding site]
Evidence:
  • Structure:1CFZ_A; E. coli Hydrogenase Maturating Endopeptidase HybD bound to Cd; contact residues defined by 3.5 A.
    View structure with Cn3D
  • Comment:Cd-binding site in this structure is predicted to be the same as the actual Ni-binding site
  • Comment:Replacement of the homologous metal binding residues in HycI (hydrogenase 3 processing endopeptidase) by site-directed mutagenesis suggest a role in catalysis.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #                                                     #             
1CFZ_A         4 LVLGVGNILlTDEAIGVRIVEALEqryi------lpdyVEILDGGTaGMELLGDMan--rdHLIIADAivskknaPGTMM 75
gi 88804049    9 LVAGVGNELkQDDAFGIEFAKKFRdavs------hldhIMVMEVGIgGIHLVQELhag-ydILILADAvaw-geeAGHIY 80
gi 111021581   8 LVAGVGNIFfGDDGFGPEVLRGVAtrtl-------ppgVRAVDFGIrGTHLAYELldg-wgALLLVDAvpg-rgePGALR 78
gi 116625612   6 LVAGVGNIFlGDDAFGSEVARRMLnekw-------pedVRVVDFGIrGFDLTFALleg-ydTVILVDAtpr-ggaPGTLY 76
gi 111221820  14 LVAGVGNIFlGDDGFGVEVVRRLDpanl-------pgeVDVADYGIrGLHLAFALldgrydTVILVDAlps-depPGTLT 85
gi 120403400  13 LVAGIGNIFlGDDGFGPEVIRRIPhrla-------gpcVRLKDYGIrGMHLAYDLlgp-wsALVLVDAvpd-rgaPGTVH 83
gi 38637735    5 LVAGIGNVFlGDDGFGVEVVQRLGarqaahalppfpegVVVADFGIrGIDLCYALldg-vdAAILVDAtqr-ggaPGSLY 82
gi 29833914   12 LVAGIGNIFlGDDGFGVETARRLAerql-------pahIEVVDIGVrGVHLAYQLldg-ydTLILVDAtar-geaPGTLY 82
gi 158314317   4 LVAGVGNILlGDDGFGVQVARHLRrtgp-------pprVTIADYGTsGLHLAFDLcsggysTVVLVDAlgr-gyePGTVS 75
gi 126434711   2 LIAGIGNIFlGDDGFGPEVLRRAAplit-------dprVRAVDYGIrGMHLAYDLlep-wdLLVLVDAlpd-rgsPGTLH 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                           #                                            
1CFZ_A        76 ILRd----------EEVPALftnk--------ispHQLGLADVLSALrftg-----efpkKLTLVGVIPESLeph----- 127
gi 88804049   81 FREm----------EKVSDIeempvfekrtfladmHYTNPIRALMLAkalk-----vlpnEVYILGCEAAQHddf----- 140
gi 111021581  79 AFEvg--------pDSVPAApl-----------daHSMDPGAVFGSLralg-----gtlpRTVVLGCQVANTgeg----- 129
gi 116625612  77 TIE-----------PELDDGeage--------vatHGMNPMRVLAMAkhmg-----aewkRLLVVGCEPAHDavnd---g 129
gi 111221820  86 VLR-----------PEVGDAptgdaa----avvdaHGMSPDVVLRLVrdlg-----geigQVVVVGCRPAVVadr----- 140
gi 120403400  84 MFEad--------pETLTTPtal----------daHAMDPGAVFACLnalg-----gaapRTVVVGCEVETVeeg----- 135
gi 38637735   83 VIElpmdaqdgdgaGDPYASpvl---------mspHEMNPALVLRALrmmg-----gtcaDVVVIGCEPADFglgegeeg 148
gi 29833914   83 LIEhds-----pggGEPEGApvl----------dgHRMTPDTVLALLdtlcagtggqpprRTLIVGCEPASVeeg----- 142
gi 158314317  76 LVDl----------TDVRAPsev----------daHGMRPDVVLDLVdtlg-----ghldRVLLVGCEPASVdhq----- 125
gi 126434711  73 VFEad--------hDALCATggl----------daHAMDPAAVFASLtalg-----gappRTVVIGCEAADVteg----- 124
                        170
                 ....*....|....*....
Feature 1                           
1CFZ_A       128 -igLTPTVEAMIEPALEQV 145
gi 88804049  141 avgMSEAVEDALPKAMRKL 159
gi 111021581 130 -igLSPRVEAAVGQAVDLV 147
gi 116625612 130 gigLSEAVRPAVAEAVEVV 148
gi 111221820 141 -meLSGAVRAAVDGAVDLI 158
gi 120403400 136 -igLSETVAAAVPAAVRAV 153
gi 38637735  149 rlgLSEPVAAAVDRAVAMV 167
gi 29833914  143 -igLSPPVSDAVPEAVRLI 160
gi 158314317 126 -vgLSPPVAAAVEPAARLV 143
gi 126434711 125 -igLSPPVAAAVPEAVRAV 142

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