5FPZ,4E2G,5FPX,2PFW,5FQ0


Conserved Protein Domain Family
cupin_KdgF

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cd02238: cupin_KdgF 
pectin degradation protein KdgF and related proteins, cupin domain
This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.
Statistics
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PSSM-Id: 380366
Aligned: 216 rows
Threshold Bit Score: 97.5397
Created: 3-Feb-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1: metal binding site [ion binding site], 4 residue positions
Conserved feature residue pattern:H H Q HClick to see conserved feature residue pattern help
Evidence:
  • Structure:5FPX: Yersinia enterocolitica pectin degrading protein KdgF binds nickel; contacts at 4.0A
  • Comment:The four-coordinate metallocenter usually includes three histidines and one glutamate; however, proteins in this subfamily may bind metal via different amino acids.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                 # #    #                            
5FPZ_A      4 FFINDETPWEElg--nGIKRKVMTWSddLMMVCVHFDkgAIGVAHKHdiHDQIAYVAAgSFEVEIe--gQKRILKaGDAY 79  Yersinia enterocol...
5FPX_A      7 FFINDETPWEElg--nGIKRKVMTWSddLMMVCVHFDkgAIGVAHKHdiHDQIAYVAAgSFEVEIe--gQKRILKaGDAY 82  Yersinia enterocol...
KKM10353    2 SNSTTSIRVTVl---pGVTRETLATGerLMVVRFTFDagAEIPLHRHp-HEQSSYVERgCLKYVVg--gVEHILKpGDSL 75  Clostridiales bact...
PKL41461    2 FVFRDKLKETDfg--hGIKLTDLGGNgnMNVLHWNTPagTVSPAHEHp-EEQFGYLLQgSFEVTIg--dEKAVLKaGDSY 76  Candidatus Rifleba...
AAV48095    6 QAACETVEAVD-----GVHLTQMAVGeeMSVQQFHIEpgAAVPEHSHr-HEQVGYVVKgTFTFHVn--gEEYVIGpGDSY 77  Haloarcula marismo...
ERG87904    3 QVDFDPSQLVEaa--dGVYLQQLATAeeMSMQYVLIEpgGVAPMHKHr-HEQSGFILQgTPTFRIgeekKEFMLAaNQSY 79  halophilic archaeo...
ESS06885    3 VIPVSAERTTEvl--dGVHLAQAAAGerASVQHFRIEpgATVDRHAHe-NEQLGWLAAgSLVFRLd--gETVTVEaGDSY 77  uncultured archaeo...
PSP61248    1 MDRVTEAEREQrevaaDVYLADLAAGerAGMKHWRVEpgATLPTHRHe-NEQIGYVISgTLVARIe--gEEHRLEaGDSY 77  Halobacteriales ar...
PSP68809    4 VVPADNETVEVa---eGVHLTQLAIGerMSIQHLRMEpgAEVPMHDHh-HEQLGFVYEgTQTFLLdd-dETVDIDaGESY 78  Halobacteriales ar...
PSP70100    1 METVSTAERETiaatdGVSVTVLASGeaMNVQAFTIDpgASVPAHSHh-HEQAGYLFAgHATFVLd--dMEHEVGpEGSY 77  Halobacteriales ar...
Feature 1            #                       
5FPZ_A     80 RAVkNEMHGAVSle-dNSILIDTFNPKRDDF 109 Yersinia enterocolitica subsp. enterocolitica 8081
5FPX_A     83 RAVkNEMHGAVSle-dNSILIDTFNPKRDDF 112 Yersinia enterocolitica subsp. enterocolitica 8081
KKM10353   76 VISpDVPHQATAl--eETVDINSFSPLREDY 104 Clostridiales bacterium PH28_bin88
PKL41461   77 FIPgGVSHQFKLl--eDCLAIDIFSPRRPVP 105 Candidatus Riflebacteria bacterium HGW-Riflebacteria-1
AAV48095   78 VVPsEEPHEARNdgeePVRGIDVFSPPRPNP 108 Haloarcula marismortui ATCC 43049
ERG87904   80 DLPgNVYHEVENegdvPVRNIDMFAPPRGHP 110 halophilic archaeon J07HX5
ESS06885   78 AIGgGERHGAHNrgdeDAVGVEVFVPPRESP 108 uncultured archaeon A07HB70
PSP61248   78 AFPsEELHGAENrgdePAVGIGVLSPPRDEP 108 Halobacteriales archaeon QH_8_64_26
PSP68809   79 HLEsEEPHAALNrgdeTMYAIDIFSPPRPNP 109 Halobacteriales archaeon QH_6_68_27
PSP70100   78 AIPaDETHAVENrgdtMVRGVECFSPPRPHP 108 Halobacteriales archaeon QH_9_66_26

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