1RHY,2F1D,2AE8


Conserved Protein Domain Family
IGPD

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cd07914: IGPD 
Click on image for an interactive view with Cn3D
Imidazoleglycerol-phosphate dehydratase
Imidazoleglycerol-phosphate dehydratase (IGPD; EC 4.2.1.19) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites. IGPD enzymes are monofunctional in fungi, plants, archaea and some eubacteria while they are encoded as bifunctional enzymes in other eubacteria, such that the enzyme is fused to histidinol-phosphate phosphatase, the penultimate enzyme of the histidine biosynthesis pathway. The histidine biosynthesis pathway is a potential target for development of herbicides, and IGPD is a target for the triazole phosphonate herbicides.
Statistics
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PSSM-Id: 153419
View PSSM: cd07914
Aligned: 141 rows
Threshold Bit Score: 225.742
Threshold Setting Gi: 122381894
Created: 29-Sep-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:putative active site pocket [active site]
Evidence:
  • Comment:These active site residues are inferred from manual docking experiments where the putative diazafulvene intermediate is docked into the metal-binding cavity.
  • Comment:IGPD is inactive as a trimer. In the presence of divalent cations, it assembles into an active 24-mer with 4-3-2 symmetry, and 24 active sites. Within the assembled enzyme, each monomer contributes residues to three separate active sites.
  • Structure:2F1D_D/G/H: Arabidopsis thaliana IGPD, showing one active site involving three subunits bound with two manganese ions and a sulfate ion; contact distance at 4A.
    View structure with Cn3D
  • Comment:The sulfate ion represents the substrate's phosphate moiety.
  • Comment:Two trimers participate at each active site. One trimer contributes residues from two subunits and the other trimer contributes residues from a single subunit.
  • Structure:2F1D: Arabidopsis thaliana IGPD, showing a monomer contributing residues to three active sites; contact distance at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                #                              #   #  ##                 ##  #          
1RHY_B         6 ASVERTTSEThiSCTIDLDHipgvteQKINVSTGIGFLDHMFTALAKHggMSLQLQCkgDLHIDDHHTAEDCALALGEAF 85  Filobasidiella ...
2F1D_G        13 GEVKRVTKETnvSVKINLDGt-----GVADSSSGIPFLDHMLDQLASHglFDVHVRAtgDVHIDDHHTNEDIALAIGTAL 87  thale cress
Q64RE9       186 AEIRRTTKETdiLVALNLDGk-----GTCDISTGLGFFDHMLEQIGKHsgMDLTIRVkgDLEVDEHHTIEDTAIALGECI 260 Bacteroides sp....
B4STN9       171 AVVQRDTKETkiRVELDLDRa-----GDARIDTGLPFFDHMLEQIGKHggFALDIQAegDLHIDEHHTIEDTGLALGQAL 245 Stenotrophomona...
Q5ZW89       166 ASVQRKTKETtiDLSVQLDSd-----QTSVIDTPIPFFTHMLEQVAKHggFDLRLQAsgDLEVDEHHLIEDTAIALGEAI 240 Legionella pneu...
YP_001676787 171 AEIKRVTNETdiIVKVNLDVp-----GTREIETGLGFFDHMLDQIVKHagISAVIKAkgDLHIDDHHCVEDVAITLSQAI 245 Francisella phi...
YP_003148780 173 ATVERNTSETriRVSVDLDRp-----APAKVSTGLGFFDHMLDQLGKHggFALEVETagDLHIDEHHTVEDTGLAIGQAL 247 Kytococcus sede...
A1W1K1       167 ASYQRTTKETdiKVKVCLNG------GKISIKTGIDFFDHMLEQIAVHggIGLEISCkgDLEIDEHHSVEDVALALGACI 240 Campylobacter j...
ZP_00951688  213 ATVRRVTKETeiTLSVDLDR------EGAEIETGNAFFDHMLEQIARHggIALSVSCqgDLEVDAHHTIEDVCLALGEGL 286 Oceanicaulis al...
ZP_04771277  313 GEVLRDTKETriSAIVDLDTp-----KPVKIHTGIGFFDHMLDQVATHggFSLQLSCqgDLEIDGHHTIEDCMLAFGQAL 387 Asticcacaulis e...
Feature 1                   #       ##            #                       #                      
1RHY_B        86 KKALgeRKGIKRYGYAYAPLDeSLSRAVIDISSRPYFMCHLPFtREKVGDLSTEMVSHLLQSFAFaagVTLHIDsIRGEN 165 Filobasidiella ...
2F1D_G        88 LKALgeRKGINRFGDFTAPLDeALIHVSLDLSGRPYLGYNLEIpTQRVGTYDTQLVEHFFQSLVNtsgMTLHIRqLAGEN 167 thale cress
Q64RE9       261 YQALgsKRGIERYGYALPMDD-CLCRVCLDFGGRPWLVWDAEFkREKIGEMPTEMFLHFFKSLSDaakMNLNIK-AEGQN 338 Bacteroides sp....
B4STN9       246 REALgdKRGIGRYGFTLPMDE-TLASAALDFSGRPYFVFEGEFkRERVGDMPTELVPHFFRSLCDasgLNLNLQ-VRGDN 323 Stenotrophomona...
Q5ZW89       241 RTALgdKWGINRYGYTLPMDE-SLATIAIDISGRSFCDFKGQFtREFIGGMATEMIPHFFQSLSSalgATIHIE-VTGTN 318 Legionella pneu...
YP_001676787 246 AQALgdKYGINRYGFLLPMDE-ALVEIALDLSGRNYCSFEANFdREMVGDLSVELVKHFFVSFAEglkATLHIK-VTGEN 323 Francisella phi...
YP_003148780 248 REALgdKRGIGRYGFTLPMDE-SLATAAIDFSGRPYLVFDCTFtREVVGDLPTEMVEHFWRSLCEaagLTLNLS-VQAEN 325 Kytococcus sede...
A1W1K1       241 KKALgdKIGIARYGFALPMDE-CLASCAMDFCNRPHLVYKAKFkKSHLGALSTEMIEHFFYSLSYamgVSLHLK-VKGKN 318 Campylobacter j...
ZP_00951688  287 RKALgdKRGIGRFGFELPMDE-TRAGVWIDLSGRPYAVFEGEIpGERVGDFPVEMCPHAFRSIAEslkAALHVK-VEGEN 364 Oceanicaulis al...
ZP_04771277  388 KQALgdRVGMARFGFVLPMDE-TEAKVSIDISGRAFCVFNGAFeASHIGDYPTEMTGHAFRSLSEalgASIHVE-VEGEN 465 Asticcacaulis e...
Feature 1         ##  #                               
1RHY_B       166 NHHIAESAFKALALAIRMAISRTgg--ddVPSTKGVL 200 Filobasidiella neoformans
2F1D_G       168 SHHIIEATFKAFARALRQATETDprrggtIPSSKGVL 204 thale cress
Q64RE9       339 EHHKIEGIFKALARALKMALKRDiyh-feLPSSKGVL 374 Bacteroides sp. 3_2_5
B4STN9       324 DHHKVEACFKALARALRPALARQgt---aLPTTKGAL 357 Stenotrophomonas maltophilia R551-3
Q5ZW89       319 HHHMIEACFKVLGRALRQACSRTnn---yLPSTKGVL 352 Legionella pneumophila subsp. pneumophila str. Philadelphia 1
YP_001676787 324 THHMIEACFKGLGKVLKQAIAKNgi--deIPSSKGVL 358 Francisella philomiragia subsp. philomiragia ATCC 25017
YP_003148780 326 DHHRIEVGFKAVARALRQAIARSgg--seLPSTKGML 360 Kytococcus sedentarius DSM 20547
A1W1K1       319 DHHKAEGLFKAFAKALKMAVKIEse---nLASSKGVI 352 Campylobacter jejuni subsp. jejuni 81-176
ZP_00951688  365 AHHMIESTFKAFGRALRMAVRVEgd---aLPSTKGVL 398 Oceanicaulis alexandrii HTCC2633
ZP_04771277  466 DHHKVEACFKALGRALRMATRIEgd---aLPSTKGML 499 Asticcacaulis excentricus CB 48

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