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: 2-Oct-2020
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:
Feature 1                                                   #                                    
2JLC_A        33 AVILEALTRhgVRHICIAPGSRSTPLTLaaaensaFIHHTHFDERGLGHLALGLAKVSkqpVAVIVTSGTAVANLYPALI 112 Escherichia coli
2JLA_A        14 AVILEALTRhgVRHICIAPGSRSTPLTLaaaensaFIHHTHFDERGLGHLALGLAKVSkqpVAVIVTSGTAVANLYPALI 93  Escherichia coli
Q89YN0         9 LQLVALLEAhgITKVVLCPGSRNAPIVHtlsthpgFTCYAMTDERSAGYFAIGLALNGghpAAVCCTSGTALLNLHPAVA 88  Bacteroides the...
YP_001093536  11 QLLISLLKQhgVRYVVASPGNTNTAFIGsiqgdqyFTIFSAVDERSAAYMACGIAAETgetVVISCTGATASRNYLPGMT 90  Shewanella loih...
ZP_02417635    9 QILLKLLKEykIKDVVLSPGGSNAPIVKsfeydkeFNCYSVVDERNAAYVALGMAQQLrrpVACVCTAGTAVSNYLPGIT 88  Anaerostipes ca...
ZP_03302455   13 LVLMALLKEygIKKVVASPGTGNMALVVsmqhdpyFEMYSCVDERSAAYMACGIAAESgepIVVTCTEATASRNYLPGLT 92  Bacteroides dor...
ZP_03168130    9 QILISLLKQfnISHVVLSPGTRNTALAGsiendpfFHCYSIVDERSAGYFALGLSEALdepVCVSCTAATATCNYLPAMK 88  Ruminococcus la...
NP_695441      9 SIVTRLLKSngINHVVISPGGTNIALIKaiqddpfFICHSVVDERSAAYFAIGVYLQTgspVALCCTSAQATRNYIPGLT 88  Bifidobacterium...
ZP_01121325   10 HLVVAYCKSagVRQVVLSPGSRNAPLVLgftsdpyFECFSVVDERSAAFFALGLSQQSgnpTALVCTSGSALLNYYPAVA 89  Robiginitalea b...
A6H070        10 QSIIEICNTkgLHHIVISPGSRNAPLTIgftnnpvFTCYSIADERCAAFFALGIAQQLkkpVALVCTSGSALLNYYPAFA 89  Flavobacterium ...
Feature 1                                                                                        
2JLC_A       113 EAGLTGEKLILLTADRPPElidcgANQAIRQPGMFASHPTHSISLPrptqd--------------------------ipa 166 Escherichia coli
2JLA_A        94 EAGLTGEKLILLTADRPPElidcgANQAIRQPGXFASHPTHSISLPrptqd--------------------------ipa 147 Escherichia coli
Q89YN0        89 EAYYQNIPLVVISADRPAAwigqmAGQTLPQPGVFQTLVKKSVNLPeiqteed-----------------------ewyc 145 Bacteroides the...
YP_001093536  91 EAYYRKLPVIAVTSSQPIAnighlSAQLLDRTVIPKDVAKLSVNLPivkdndd-----------------------vwec 147 Shewanella loih...
ZP_02417635   89 EAFYQNVPVVAITSDGLSSlldqlELQKIDQVGIFKGCIKKEVALPavktemd-----------------------ewyc 145 Anaerostipes ca...
ZP_03302455   93 EAFYRKLPILAIMTGRGENrtgsyEPQSIDNAVLPNDVAKYRVNIPvcrnhkd-----------------------eriv 149 Bacteroides dor...
ZP_03168130   89 EAYERNIQLVALTADQNPYemfhmEDQCIDQVDMFHGYVKLAVDVPkvmndad-----------------------ywyc 145 Ruminococcus la...
NP_695441     89 EAYYKHVPLLAICMQKHPRftyqeYMQAPDQSSLPADSVKKSFVAPyisdind-----------------------vyhs 145 Bifidobacterium...
ZP_01121325   90 EAYYSRIPLLVLSADRPVYkidigDGQTIRQDGVYGNHIGFQGNLQqdvthapasirweggrepgdprslhemqarilae 169 Robiginitalea b...
A6H070        90 EAFYSQIPLVVISADRPQSkidigDGQTIRQENVFANHSLYNANLVenvs----------------------------ee 141 Flavobacterium ...
Feature 1                                 
2JLC_A       167 rwLVSTIDHALGTLHaGGVHINCPF 191 Escherichia coli
2JLA_A       148 rwLVSTIDHALGTLHaGGVHINCPF 172 Escherichia coli
Q89YN0       146 nrLVNEALLETNHHGkGPVHINIPI 170 Bacteroides thetaiotaomicron VPI-5482
YP_001093536 148 eiKINQAILESCRHGgGPVHINLPT 172 Shewanella loihica PV-4
ZP_02417635  146 nrLVNEALLELNHHGtGPVHINIPI 170 Anaerostipes caccae DSM 14662
ZP_03302455  150 ttKLNEAINNLYTGGgGPVCVVMES 174 Bacteroides dorei DSM 17855
ZP_03168130  146 nrRMNEAFLELDHHGkGPIQINYHM 170 Ruminococcus lactaris ATCC 29176
NP_695441    146 irVINQAIQELTHNGlGPVQLCIPW 170 Bifidobacterium longum NCC2705
ZP_01121325  170 neARVQAALQTAMEDhLPVHLNIPF 194 Robiginitalea biformata HTCC2501
A6H070       142 ndAKIQEAIHLATTKkGPVHINVPF 166 Flavobacterium psychrophilum JIP02/86

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