1CFZ,2I8L,2E85


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: 2-Oct-2020
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:
Feature 1                    #                                                     #             
1CFZ_A         4 LVLGVGNILlTDEAIGVRIVEALEqryi------lpdyVEILDGGTaGMELLGDMan--rdHLIIADAivskknaPGTMM 75  Escherichia coli
ZP_01119569    9 LVAGVGNELkQDDAFGIEFAKKFRdavs------hldhIMVMEVGIgGIHLVQELhag-ydILILADAvaw-geeAGHIY 80  Robiginitalea b...
YP_704553      8 LVAGVGNIFfGDDGFGPEVLRGVAtrtl-------ppgVRAVDFGIrGTHLAYELldg-wgALLLVDAvpg-rgePGALR 78  Rhodococcus sp....
YP_827768      6 LVAGVGNIFlGDDAFGSEVARRMLnekw-------pedVRVVDFGIrGFDLTFALleg-ydTVILVDAtpr-ggaPGTLY 76  Solibacter usit...
YP_712614     14 LVAGVGNIFlGDDGFGVEVVRRLDpanl-------pgeVDVADYGIrGLHLAFALldgrydTVILVDAlps-depPGTLT 85  Frankia alni AC...
YP_953229     13 LVAGIGNIFlGDDGFGPEVIRRIPhrla-------gpcVRLKDYGIrGMHLAYDLlgp-wsALVLVDAvpd-rgaPGTVH 83  Mycobacterium v...
NP_942709      5 LVAGIGNVFlGDDGFGVEVVQRLGarqaahalppfpegVVVADFGIrGIDLCYALldg-vdAAILVDAtqr-ggaPGSLY 82  Ralstonia eutro...
NP_828548     12 LVAGIGNIFlGDDGFGVETARRLAerql-------pahIEVVDIGVrGVHLAYQLldg-ydTLILVDAtar-geaPGTLY 82  Streptomyces av...
YP_001506825   4 LVAGVGNILlGDDGFGVQVARHLRrtgp-------pprVTIADYGTsGLHLAFDLcsggysTVVLVDAlgr-gyePGTVS 75  Frankia sp. EAN...
YP_001070402   2 LIAGIGNIFlGDDGFGPEVLRRAAplit-------dprVRAVDYGIrGMHLAYDLlep-wdLLVLVDAlpd-rgsPGTLH 72  Mycobacterium s...
Feature 1                                           #                                            
1CFZ_A        76 ILRd----------EEVPALftnk--------ispHQLGLADVLSALrftg-----efpkKLTLVGVIPESLeph----- 127 Escherichia coli
ZP_01119569   81 FREm----------EKVSDIeempvfekrtfladmHYTNPIRALMLAkalk-----vlpnEVYILGCEAAQHddf----- 140 Robiginitalea b...
YP_704553     79 AFEvg--------pDSVPAApl-----------daHSMDPGAVFGSLralg-----gtlpRTVVLGCQVANTgeg----- 129 Rhodococcus sp....
YP_827768     77 TIE-----------PELDDGeage--------vatHGMNPMRVLAMAkhmg-----aewkRLLVVGCEPAHDavnd---g 129 Solibacter usit...
YP_712614     86 VLR-----------PEVGDAptgdaa----avvdaHGMSPDVVLRLVrdlg-----geigQVVVVGCRPAVVadr----- 140 Frankia alni AC...
YP_953229     84 MFEad--------pETLTTPtal----------daHAMDPGAVFACLnalg-----gaapRTVVVGCEVETVeeg----- 135 Mycobacterium v...
NP_942709     83 VIElpmdaqdgdgaGDPYASpvl---------mspHEMNPALVLRALrmmg-----gtcaDVVVIGCEPADFglgegeeg 148 Ralstonia eutro...
NP_828548     83 LIEhds-----pggGEPEGApvl----------dgHRMTPDTVLALLdtlcagtggqpprRTLIVGCEPASVeeg----- 142 Streptomyces av...
YP_001506825  76 LVDl----------TDVRAPsev----------daHGMRPDVVLDLVdtlg-----ghldRVLLVGCEPASVdhq----- 125 Frankia sp. EAN...
YP_001070402  73 VFEad--------hDALCATggl----------daHAMDPAAVFASLtalg-----gappRTVVIGCEAADVteg----- 124 Mycobacterium s...
Feature 1                           
1CFZ_A       128 -igLTPTVEAMIEPALEQV 145 Escherichia coli
ZP_01119569  141 avgMSEAVEDALPKAMRKL 159 Robiginitalea biformata HTCC2501
YP_704553    130 -igLSPRVEAAVGQAVDLV 147 Rhodococcus sp. RHA1
YP_827768    130 gigLSEAVRPAVAEAVEVV 148 Solibacter usitatus Ellin6076
YP_712614    141 -meLSGAVRAAVDGAVDLI 158 Frankia alni ACN14a
YP_953229    136 -igLSETVAAAVPAAVRAV 153 Mycobacterium vanbaalenii PYR-1
NP_942709    149 rlgLSEPVAAAVDRAVAMV 167 Ralstonia eutropha H16
NP_828548    143 -igLSPPVSDAVPEAVRLI 160 Streptomyces avermitilis MA-4680
YP_001506825 126 -vgLSPPVAAAVEPAARLV 143 Frankia sp. EAN1pec
YP_001070402 125 -igLSPPVAAAVPEAVRAV 142 Mycobacterium sp. JLS

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