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(-) Description

Title :  CRYSTAL STRUCTURE OF IPP ISOMERASE AT P43212
 
Authors :  T. Wada, S. -Y. Park, R. H. Tame, S. Kuramitsu, S. Yokoyama, Riken Struc Genomics/Proteomics Initiative (Rsgi)
Date :  08 Mar 04  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Biol. Unit 2:  A,B,C,D  (1x)
Keywords :  Tim Barrel, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wada, S. -Y. Park, R. H. Tame, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Ipp Isomerase At P43212
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD
Biological Unit 2 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1FMN8Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE40Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:65 , MSE A:66 , THR A:67 , GLY A:94 , SER A:95 , ASN A:123 , HIS A:152 , LYS A:187 , VAL A:189 , GLY A:190 , THR A:217 , TRP A:219 , GLY A:263 , GLY A:264 , TYR A:266 , ALA A:285 , ARG A:286BINDING SITE FOR RESIDUE FMN A 501
2AC2SOFTWAREALA B:65 , MSE B:66 , THR B:67 , GLY B:94 , SER B:95 , ASN B:123 , HIS B:152 , LYS B:187 , VAL B:189 , GLY B:190 , THR B:217 , TRP B:219 , GLY B:263 , GLY B:264 , TYR B:266 , ALA B:285 , ARG B:286BINDING SITE FOR RESIDUE FMN B 502
3AC3SOFTWAREALA C:65 , MSE C:66 , THR C:67 , GLY C:94 , SER C:95 , ASN C:123 , HIS C:152 , LYS C:187 , VAL C:189 , GLY C:190 , THR C:217 , TRP C:219 , GLY C:263 , GLY C:264 , TYR C:266 , ALA C:285 , ARG C:286BINDING SITE FOR RESIDUE FMN C 503
4AC4SOFTWAREALA D:65 , MSE D:66 , THR D:67 , SER D:95 , ASN D:123 , HIS D:152 , LYS D:187 , VAL D:189 , GLY D:190 , THR D:217 , TRP D:219 , GLY D:263 , GLY D:264 , TYR D:266 , ALA D:285 , ARG D:286BINDING SITE FOR RESIDUE FMN D 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VCG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VCG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VCG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VCG)

(-) Exons   (0, 0)

(no "Exon" information available for 1VCG)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:311
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:324
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
           IDI2_THET2     9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcga_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.........hhh.eee........hhhhh...ee....ee...eeeeee.------hhhhhhhhhhhhhhh.eeeeee.hhhh...-------.........eeee.hhhhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhh......eeee......hhhhhhh.......eee.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcg A   9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmT------ERINLALAEAAEALGVGmmLGSGRILLERP-------VRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    18        28        38        48        58       ||-     |  78        88  ||    98    |    -  |    118       128       138    |  148       158       168       178      |188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
                                                                                    66-MSE  74               91-MSE     103     111                             143-MSE                                   185-MSE                                                                                                                                               
                                                                                     67                       92-MSE                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:318
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:324
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
           IDI2_THET2     9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcgb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.........hhh.eee........hhhhh...ee....ee...eeeeee.------hhhhhhhhhhhhhhh.eeeeee.hhhh.hhhhhhhh..........eeee.hhhhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhh......eeee......hhhhhhh.......eee.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcg B   9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmT------ERINLALAEAAEALGVGmmLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    18        28        38        48        58       ||-     |  78        88  ||    98       108       118       128       138    |  148       158       168       178      |188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
                                                                                    66-MSE  74               91-MSE                                             143-MSE                                   185-MSE                                                                                                                                               
                                                                                     67                       92-MSE                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:316
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:324
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
           IDI2_THET2     9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcgc_ C: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.........hhh.eee........hhhhh...ee....ee...eeeeee.------hhhhhhhhhhhhhhh.eeeeee.hhhh.hhhhh.--..........eeee.hhhhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhh......eeee......hhhhhhh.......eee.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcg C   9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmT------ERINLALAEAAEALGVGmmLGSGRILLERPEALR--RVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    18        28        38        48        58       ||-     |  78        88  ||    98        |- |     118       128       138    |  148       158       168       178      |188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
                                                                                    66-MSE  74               91-MSE         107  |                              143-MSE                                   185-MSE                                                                                                                                               
                                                                                     67                       92-MSE           110                                                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:311
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:324
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
           IDI2_THET2     9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcgd_ D: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.........hhh.eee........hhhhh...ee....ee...eeeeee.------hhhhhhhhhhhhhhh.eeeeee.hhhh...-------.........eeee.hhhhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhh......eeee......hhhhhhh.......eee.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcg D   9 KHLEACLEGEVAYQKTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmT------ERINLALAEAAEALGVGmmLGSGRILLERP-------VRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    18        28        38        48        58       ||-     |  78        88  ||    98    |    -  |    118       128       138    |  148       158       168       178      |188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
                                                                                    66-MSE  74               91-MSE     103     111                             143-MSE                                   185-MSE                                                                                                                                               
                                                                                     67                       92-MSE
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VCG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VCG)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IDI2_THET2 | Q746I8)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004452    isopentenyl-diphosphate delta-isomerase activity    Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IDI2_THET2 | Q746I8: 1vcf

(-) Related Entries Specified in the PDB File

1p0k
1p0n
1vcf THE SAME PROTEIN AT I422 RELATED ID: TTK003001255.2 RELATED DB: TARGETDB