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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IMP BIOSYNTHESIS PROTEIN PURP FROM THERMOCOCCUS KODAKARAENSIS
 
Authors :  R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  29 Mar 07  (Deposition) - 10 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nysgxrc, Psi-Ii, Imp Biosynthesis, Atp Binding Protein, Purp, 10188D, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
Crystal Structure Of An Imp Biosynthesis Protein Purp From Thermococcus Kodakaraensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C
    EC Number: 6.3.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURP, TK0431
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:129 , GLU A:145 , ARG A:164 , PHE A:165 , ILE A:166 , TYR A:170 , TYR A:172 , LEU A:194 , TYR A:209 , ILE A:263 , HOH A:409 , HOH A:436 , HOH A:438 , HOH A:454 , ARG C:201BINDING SITE FOR RESIDUE ATP A 400
2AC2SOFTWAREARG A:201 , PHE B:129 , GLU B:145 , ARG B:164 , PHE B:165 , ILE B:166 , TYR B:170 , TYR B:172 , LEU B:194 , TYR B:209 , ILE B:263 , HOH B:405 , HOH B:427 , HOH B:439 , HOH B:441 , HOH B:458 , HOH B:470BINDING SITE FOR RESIDUE ATP B 400
3AC3SOFTWAREARG B:201 , PHE C:129 , GLU C:145 , ARG C:164 , PHE C:165 , ILE C:166 , TYR C:170 , TYR C:172 , LEU C:194 , TYR C:209 , ILE C:263 , HOH C:404 , HOH C:414 , HOH C:415 , HOH C:428 , HOH C:433 , HOH C:438 , HOH C:457BINDING SITE FOR RESIDUE ATP C 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PBZ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:123 -Pro A:124
2Lys B:123 -Pro B:124
3Lys C:123 -Pro C:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PBZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PBZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PBZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:293
 aligned with Q5JD28_THEKO | Q5JD28 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q5JD28_THEKO     2 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEMTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRIEGPRGGSGHFIVEGSELEERLSTLEEPYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTMRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSMGRRIARELRLAEEEDRLEEVVT 310
               SCOP domains d2pbza1 A:4-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                d2pbza2 A:100-312 5-formaminoimid            azole-4-ca    rboxamide ribonucleotide synthetase PurP                                                                                                                   SCOP domains
               CATH domains 2pbzA01 A:4-85  [code=3.40.50.20, no name defined]                                2pbzA02 A:86-113,A:168-312  2pbzA03 A:114-167 A            TP-grasp f    old, A do2pbzA02 A:86-113,A:168-312 ATP-grasp fold, B domain                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...eeeee...hhhhhhh.....eeee..................hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.................eeee.------------..ee......----..eeee.....eeeeeeeee....eeeeeeeeeeee................eeeeee.ee...hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeee....hhhhh...hhhhhh....hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbz A   4 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEmTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRI------------EGSELEERLS----PYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTmRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSmGRRIARELRLAEEEDRLEEVVT 312
                                    13        23        33        43        53|       63        73        83        93       103       113       123        |-         - |     153|    | 163       173       183       193       203       213       223       233    |  243       253       263       273       283      |293       303         
                                                                             54-MSE                                                                       132          145      154  159                                                                            238-MSE                                             290-MSE                  


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with Q5JD28_THEKO | Q5JD28 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q5JD28_THEKO     2 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEMTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRIEGPRGGSGHFIVEGSELEERLSTLEEPYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTMRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSMGRRIARELRLAEEEDRLEEVVT 310
               SCOP domains d2pbzb1 B:4-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                d2pbzb2 B:100-312 5-formaminoimid            azole-4-ca    rboxamide ribonucleotide synthetase PurP                                                                                                                   SCOP domains
               CATH domains 2pbzB01 B:4-85  [code=3.40.50.20, no name defined]                                2pbzB02 B:86-113,B:168-312  2pbzB03 B:114-167 A            TP-grasp f    old, A do2pbzB02 B:86-113,B:168-312 ATP-grasp fold, B domain                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...eeeee...hhhhhhh.....eeee..................hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..................eeee.------------..ee......----..eeee.....eeeeeeeee....eeeeeeeeeeee................eeeeee.ee...hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeee....hhhhh...hhhhhh....hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbz B   4 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEmTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRI------------EGSELEERLS----PYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTmRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSmGRRIARELRLAEEEDRLEEVVT 312
                                    13        23        33        43        53|       63        73        83        93       103       113       123        |-         - |     153|    | 163       173       183       193       203       213       223       233    |  243       253       263       273       283      |293       303         
                                                                             54-MSE                                                                       132          145      154  159                                                                            238-MSE                                             290-MSE                  


Chain C from PDB  Type:PROTEIN  Length:293
 aligned with Q5JD28_THEKO | Q5JD28 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q5JD28_THEKO     2 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEMTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRIEGPRGGSGHFIVEGSELEERLSTLEEPYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTMRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSMGRRIARELRLAEEEDRLEEVVT 310
               SCOP domains d2pbzc1 C:4-99 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP                d2pbzc2 C:100-312 5-formaminoimid            azole-4-ca    rboxamide ribonucleotide synthetase PurP                                                                                                                   SCOP domains
               CATH domains 2pbzC01 C:4-85  [code=3.40.50.20, no name defined]                                2pbzC02 C:86-113,C:168-312  2pbzC03 C:114-167 A            TP-grasp f    old, A do2pbzC02 C:86-113,C:168-312 ATP-grasp fold, B domain                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...eeeee...hhhhhhh.....eeee..................hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..................eeee.------------..ee......----..eeee.....eeeeeeeee....eeeeeeeeeeee................eeeeee.ee...hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeee....hhhhh...hhhhhh....hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbz C   4 IVSTIASHSSLQILLGAKKEGFKTRLYVSPKRRPFYSSLPIVDDLVVAEEmTSILNDDGIVVPHGSFVAYLGIEAIEKAKARFFGNRRFLKWETTFELQDKALEGAGIPRVEVVEPEDAKPDELYFVRI------------EGSELEERLS----PYRVERFIPGVYLYVHFFYSPILERLELLGVDERVLIADGNARWPVKPLPYTIVGNRAIALRESLLPQLYDYGLAFVRTmRELEPPGVIGPFALHFAYDGSFKAIGIASRIDGGSNADHWYSELYWGERLSmGRRIARELRLAEEEDRLEEVVT 312
                                    13        23        33        43        53|       63        73        83        93       103       113       123        |-         - |     153|    | 163       173       183       193       203       213       223       233    |  243       253       263       273       283      |293       303         
                                                                             54-MSE                                                                       132          145      154  159                                                                            238-MSE                                             290-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 9)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PBZ)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q5JD28_THEKO | Q5JD28)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016879    ligase activity, forming carbon-nitrogen bonds    Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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.
biological process
    GO:0006188    IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.

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