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(-) Description

Title :  PYRUVATE PHOSPHATE DIKINASE (PPDK) TRIPLE MUTANT R219E/E271R/S262D ADAPTS A SECOND CONFORMATIONAL STATE
 
Authors :  K. Lim, R. J. Read, C. C. Chen, O. Herzberg
Date :  10 Sep 07  (Deposition) - 01 Jan 08  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phosphotransferase, Conformational Transition, Swiveling Domain, Remote Active Sites, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lim, R. J. Read, C. C. Chen, A. Tempczyk, M. Wei, D. Ye, C. Wu, D. Dunaway-Mariano, O. Herzberg
Swiveling Domain Mechanism In Pyruvate Phosphate Dikinase.
Biochemistry V. 46 14845 2007
PubMed-ID: 18052212  |  Reference-DOI: 10.1021/BI701848W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE, PHOSPHATE DIKINASE
    Chains: A
    EC Number: 2.7.9.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC184 D12
    Expression System Strain: JM101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPDK
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM SYMBIOSUM
    Organism Taxid: 1512
    Synonym: PYRUVATE, ORTHOPHOSPHATE DIKINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:617 , ASP A:769BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREARG A:461 , ASN A:539 , SER A:855BINDING SITE FOR RESIDUE SO4 A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R82)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R82)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R82)

(-) 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

(-) Exons   (0, 0)

(no "Exon" information available for 2R82)

(-) 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:872
 aligned with PPDK_CLOSY | P22983 from UniProtKB/Swiss-Prot  Length:874

    Alignment length:872
                                    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 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN 873
               SCOP domains d2r82a3 A:2-376 Pyruvate phosphate dikinase, N-terminal domain                                                                                                                                                                                                                                                                                                                         d2r82a2 A:377-509 Pyruvate phosphate dikinase, central domain                                                                        d2r82a1 A:510-873 Pyruvate phosphate dikinase, C-terminal domain                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2r82A01 A:2-109,A:197-243 ATP-grasp fold, A domain                                                          2r82A02 A:110-196  [code=1.20.80.30, no name defined]                                  2r82A01 A:2-109,A:197-243                      2r82A03 A:244-341 ATP-grasp fold, B domain                                                        2r82A04 A:342-381,A:510-531             2r82A05 A:382-507 Phosphohistidine domains of PEP-utilising enzymes                                                           --2r82A04               2r82A06 A:532-873 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------PPDK_N-2r82A03 A:10-362                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------PEP-utilizers-2r82A02 A:412-503                                                             -----------PEP-utilizers_C-2r82A01 A:515-871                                                                                                                                                                                                                                                                                                                                    -- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eeeeeee.........eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhh.......eeeeeee..........eeeeeeee......eeeeeeeee..hhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhh.eeeee.eeee..eeeeeee.hhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeee......hhhhhhhhhh...eee.....eee....eeee..eeee...eeeee....eeee..........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeee..hhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...eeeehhhhhhhhhhh.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_2      ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r82 A   2 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPEAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPDTGEKGIYGRYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN 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
   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  (3, 3)

Asymmetric Unit
(-)
Clan: PK_TIM (63)
(-)
Clan: no clan defined [family: PEP-utilizers] (11)
(-)
Clan: no clan defined [family: PPDK_N] (7)

(-) 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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  2r82
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  PPDK_CLOSY | P22983
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  2.7.9.1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1dik
1kbl THE SAME PROTEIN IN A DIFFERENT CONFORMATION
1kc7 SAME AS 1KBL BUT COMPLEXED WITH MG-PHOSPHONOPYRUVATE