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(-) Description

Title :  T453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE
 
Authors :  Z. Li, O. Herzberg
Date :  29 Aug 00  (Deposition) - 10 Jan 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Transferase, Phosphotransferase, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wei, Z. Li, D. Ye, O. Herzberg, D. Dunaway-Mariano
Identification Of Domain-Domain Docking Sites Within Clostridium Symbiosum Pyruvate Phosphate Dikinase By Amino Acid Replacement.
J. Biol. Chem. V. 275 41156 2000
PubMed-ID: 10995759  |  Reference-DOI: 10.1074/JBC.M006149200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
    Chains: A
    EC Number: 2.7.9.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PPDK
    Expression System Plasmid: PACYC184D-12
    Expression System Strain: JM 101
    Expression System Taxid: 562
    Gene: PPDK
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM SYMBIOSUM
    Organism Taxid: 1512
    Strain: JM 101
    Synonym: PPDK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:22 , PRO A:100 , GLY A:101 , MET A:103 , ARG A:337BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:617 , ASP A:620 , HOH A:1042BINDING SITE FOR RESIDUE SO4 A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEP_ENZYMES_PHOS_SITEPS00370 PEP-utilizing enzymes phosphorylation site signature.PPDK_CLOSY450-461  1A:450-461
2PEP_ENZYMES_2PS00742 PEP-utilizing enzymes signature 2.PPDK_CLOSY761-779  1A:761-779
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEP_ENZYMES_PHOS_SITEPS00370 PEP-utilizing enzymes phosphorylation site signature.PPDK_CLOSY450-461  2A:450-461
2PEP_ENZYMES_2PS00742 PEP-utilizing enzymes signature 2.PPDK_CLOSY761-779  2A:761-779
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEP_ENZYMES_PHOS_SITEPS00370 PEP-utilizing enzymes phosphorylation site signature.PPDK_CLOSY450-461  2A:450-461
2PEP_ENZYMES_2PS00742 PEP-utilizing enzymes signature 2.PPDK_CLOSY761-779  2A:761-779

(-) Exons   (0, 0)

(no "Exon" information available for 1GGO)

(-) 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:869
 aligned with PPDK_CLOSY | P22983 from UniProtKB/Swiss-Prot  Length:874

    Alignment length:873
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871   
           PPDK_CLOSY     2 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK 874
               SCOP domains d1ggoa3 A:2-376 Pyruvate phosphate dikinase, N-terminal domain                                                                                                                                                                                                                                                                                                                         d1ggoa2 A:377-505 Pyruvate phosphate dikinase, central domain                                                                    ----d1ggoa1 A:510-874 Pyruvate phosphate dikinase, C-terminal domain                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1ggoA01 A:2-109,A:199-243 ATP-grasp fold, A domain                                                          1ggoA05 A:110-198  [code=1.20.80.30, no name defined]                                    1ggoA01 A:2-109,A:199-243                    1ggoA06 A:244-341 ATP-grasp fold, B domain                                                        1ggoA02 A:342-382,A:510-531              1ggoA03 A:383-505 Phosphohistidine domains of PEP-utilising enzymes                                                        ----1ggoA02               1ggoA04 A:532-873 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..ee.....ee.eeeeeee.........eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.......eeeeeee..........eeeeeeee......eeeeeeeee..hhhhhh......ee..hhhhhh.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeee......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhh..eeee.eeee...eeeeee.hhhhhhhh......eeeee...hhhhhhhhhh..eeee......hhhhhhhhhh..eeee.....eee....eeee..eee...eeee....eee.----........hhhhhhhhhhhhh....eeee...hhhhhhhhhh.....eeeeehhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhh..hhhhhh........hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_2      ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ggo A   2 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMASHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKI----IETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK 874
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   |   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 505  510
   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  (3, 3)

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

(-) CATH Domains  (6, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (PPDK_CLOSY | P22983)
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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0050242    pyruvate, phosphate dikinase activity    Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H(+) + phosphoenolpyruvate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPDK_CLOSY | P22983: 1dik 1jde 1kbl 1kc7 2dik 2fm4 2r82

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