Conserved Protein Domain Family
H2MP_MemB-H2up

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cd06062: H2MP_MemB-H2up 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 99873
View PSSM: cd06062
Aligned: 62 rows
Threshold Bit Score: 141.053
Threshold Setting Gi: 74317398
Created: 10-Dec-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
nickel bindingputative
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         3 ILVLGVGNILlTDEAIGVRIVEALEqry---ilPDYVEILDGGTaGMELLGDMANrDHLIIADAIvsk-knAPGTMMILR 78
gi 157737666   9 ILILGIGNILfQDEGIGAHFIHYLDekyefisqENSVSLVDGGTlAQRLIPEIIKyDEVLIIDCIdai-nsKAGDVFFFD 87
gi 34557996    3 ILVLGIGNILfGDEGIGVHLSNLLKvnyr-fegPHQVDVIDGGTlAQLLIPLITSyDYVIVIDCVdag-ggKIGEVYFFD 80
gi 149194379   3 ILVLGIGNILfGDEGIGVHLVNFLEekye-fngPHKIDFVDGGTlAQRLIPIIVEyDKVFIFDTVdvd-daKIGDVYFFD 80
gi 24373656    3 ILLLGIGNVLyADEGIGVHFVNYITenyqftheSHQLEMLDGGTlAQGLIPIICQyDYLIVVDTVnan-gvDAGEVYFFD 81
gi 15611644    5 ILILGIGNILfGDEGIGVHLAHYLKrnf---sfFPSVDIVDGGTmAQQLIPLITSyEKVLILDCVsak-gvEIGSVYAFD 80
gi 163785558   4 IAIIGVGNILfKDEGIGVFIVKYLQeny---ifKPTIDLIDAGTlGFRLMEYLEDyDYIILVDTIsi--kdKPGSVFRLT 78
gi 152990711   3 TAIIGIGNILfMDEGIGVYASKYLEenf---vfDKDVEIVDGGTlGFKLMRYYQEyDKVIILDTVsi--edAPGSIYNLP 77
gi 157737673   4 NIIVGVGNMLfKDEGIGIYASEYIRqny--efdDENLEIIDGGTlGFKLMAYFQEyDNVIILDTVsi--edTAGSIYRLP 79
gi 78486375   13 IAIMGVGNILfTDEGIGIYATEFLKqny---qfSPTIDLIDGGTlGMNLIHYYQSyDHLLLLDTIsvgdanTPGEVYSLN 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
Feature 1                      #                                                          
1CFZ_A        79 dEEVPALftnkiSPHQLGLADVLSALRFTGefpKKLTLVGVIPESLe--pHIGLTPTVEAMIEPALEQVLAAL 149
gi 157737666  88 fKKVPSNinwqgSAHEVEMLQTLNMIDMNKd-lPTTHILGVIPKRVaddtTFELSSEIIQASKTMQMVVVDYL 159
gi 34557996   81 fDNVPNVitwqgSAHEVEMLQTLRMTEVNGd-lPPVKIVGVIPSIIgsetAFDLSKEVAEASVTMEKIVLNHL 152
gi 149194379  81 fLDVPECvswqgSAHEVEMLQTLEMIHMMGd-lPETKIIGVVPYVIgedtTFSITKPVLEASKLMEKILLTEL 152
gi 24373656   82 fDKAPQEidwqgSAHEVEMLQTLNMMEMVGd-rPKTFVLGVTPTVLep-mTLGLTSKVASAVPLMERTLLSHL 152
gi 15611644   81 fKDAPKEitwagSAHEVEMLHTLRLTEFLGd-lPKTFIVGLVPFVIgsetTFKLSSEMLNALETALKAIETQL 152
gi 163785558  79 aEDLAGIgsyhqTAHEVEVLQMLELTALKGk-rAETIIIGIVPENIctseIGLTKPLENEGFKTATYQVLKEL 150
gi 152990711  78 sEVLLGLgeyrkTAHEVEVVEMLEICSMLEs-iAQVNIIGIVPKDIes-vGIGLTDTMRESFASYIQTLLQEL 148
gi 157737673  80 sEVLLGLgnyrkTAHEVEIVEMLEIVSVLDs-hANVTIMGIIPEDIis-vEIGLTKKMEEKFEEYILNIIKEI 150
gi 78486375   90 sDVLQGMgqyrqTAHEVEVLQTLELGALAGe-iAQVQIIAMVPQDIet-vAFELTRPIRQNIGLFINSVIQQL 160

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