2JLC,2JLA


Conserved Protein Domain Family
TPP_PYR_MenD

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cd07037: TPP_PYR_MenD 
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Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins.
Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate (SEPHCHC) synthase (MenD) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Escherichia coli MenD (EcMenD) is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. EcMenD catalyzes a Stetter-like conjugate addition of alpha-ketoglutarate to isochorismate, leading to the formation of SEPHCHC and carbon dioxide, this addition is the first committed step in the biosynthesis of vitamin K2 (menaquinone).
Statistics
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PSSM-Id: 132920
View PSSM: cd07037
Aligned: 83 rows
Threshold Bit Score: 181.928
Threshold Setting Gi: 154508613
Created: 22-Dec-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:TPP binding site [chemical binding site]
Evidence:
  • Structure:2JLA_A/B; Escherichia coli MenD homodimer binds TPP and divalent metal ion; contacts at 3.5A
    View structure with Cn3D
  • Comment:E.coli MenD is a homotetramer (dimer-of-homodimers), having four active sites, two per dimer.
  • Comment:each TPP binds in a site lying between a PYR domain and a PP domain from different subunits.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                   #                                    
2JLC_A        33 AVILEALTRhgVRHICIAPGSRSTPLTLaaaensaFIHHTHFDERGLGHLALGLAKVSkqpVAVIVTSGTAVANLYPALI 112
2JLA_A        14 AVILEALTRhgVRHICIAPGSRSTPLTLaaaensaFIHHTHFDERGLGHLALGLAKVSkqpVAVIVTSGTAVANLYPALI 93
gi 81442596    9 LQLVALLEAhgITKVVLCPGSRNAPIVHtlsthpgFTCYAMTDERSAGYFAIGLALNGghpAAVCCTSGTALLNLHPAVA 88
gi 127512339  11 QLLISLLKQhgVRYVVASPGNTNTAFIGsiqgdqyFTIFSAVDERSAAYMACGIAAETgetVVISCTGATASRNYLPGMT 90
gi 167745508   9 QILLKLLKEykIKDVVLSPGGSNAPIVKsfeydkeFNCYSVVDERNAAYVALGMAQQLrrpVACVCTAGTAVSNYLPGIT 88
gi 212694327  13 LVLMALLKEygIKKVVASPGTGNMALVVsmqhdpyFEMYSCVDERSAAYMACGIAAESgepIVVTCTEATASRNYLPGLT 92
gi 197303083   9 QILISLLKQfnISHVVLSPGTRNTALAGsiendpfFHCYSIVDERSAGYFALGLSEALdepVCVSCTAATATCNYLPAMK 88
gi 23464838    9 SIVTRLLKSngINHVVISPGGTNIALIKaiqddpfFICHSVVDERSAAYFAIGVYLQTgspVALCCTSAQATRNYIPGLT 88
gi 88805806   10 HLVVAYCKSagVRQVVLSPGSRNAPLVLgftsdpyFECFSVVDERSAAFFALGLSQQSgnpTALVCTSGSALLNYYPAVA 89
gi 193806071  10 QSIIEICNTkgLHHIVISPGSRNAPLTIgftnnpvFTCYSIADERCAAFFALGIAQQLkkpVALVCTSGSALLNYYPAFA 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
2JLC_A       113 EAGLTGEKLILLTADRPPElidcgANQAIRQPGMFASHPTHSISLPrptqd--------------------------ipa 166
2JLA_A        94 EAGLTGEKLILLTADRPPElidcgANQAIRQPGXFASHPTHSISLPrptqd--------------------------ipa 147
gi 81442596   89 EAYYQNIPLVVISADRPAAwigqmAGQTLPQPGVFQTLVKKSVNLPeiqteed-----------------------ewyc 145
gi 127512339  91 EAYYRKLPVIAVTSSQPIAnighlSAQLLDRTVIPKDVAKLSVNLPivkdndd-----------------------vwec 147
gi 167745508  89 EAFYQNVPVVAITSDGLSSlldqlELQKIDQVGIFKGCIKKEVALPavktemd-----------------------ewyc 145
gi 212694327  93 EAFYRKLPILAIMTGRGENrtgsyEPQSIDNAVLPNDVAKYRVNIPvcrnhkd-----------------------eriv 149
gi 197303083  89 EAYERNIQLVALTADQNPYemfhmEDQCIDQVDMFHGYVKLAVDVPkvmndad-----------------------ywyc 145
gi 23464838   89 EAYYKHVPLLAICMQKHPRftyqeYMQAPDQSSLPADSVKKSFVAPyisdind-----------------------vyhs 145
gi 88805806   90 EAYYSRIPLLVLSADRPVYkidigDGQTIRQDGVYGNHIGFQGNLQqdvthapasirweggrepgdprslhemqarilae 169
gi 193806071  90 EAFYSQIPLVVISADRPQSkidigDGQTIRQENVFANHSLYNANLVenvs----------------------------ee 141
                        170       180
                 ....*....|....*....|....*
Feature 1                                 
2JLC_A       167 rwLVSTIDHALGTLHaGGVHINCPF 191
2JLA_A       148 rwLVSTIDHALGTLHaGGVHINCPF 172
gi 81442596  146 nrLVNEALLETNHHGkGPVHINIPI 170
gi 127512339 148 eiKINQAILESCRHGgGPVHINLPT 172
gi 167745508 146 nrLVNEALLELNHHGtGPVHINIPI 170
gi 212694327 150 ttKLNEAINNLYTGGgGPVCVVMES 174
gi 197303083 146 nrRMNEAFLELDHHGkGPIQINYHM 170
gi 23464838  146 irVINQAIQELTHNGlGPVQLCIPW 170
gi 88805806  170 neARVQAALQTAMEDhLPVHLNIPF 194
gi 193806071 142 ndAKIQEAIHLATTKkGPVHINVPF 166

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