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PDBsum entry 1dik

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Phosphotransferase PDB id
1dik
Jmol
Contents
Protein chain
869 a.a. *
Ligands
SO4 ×3
Waters ×416
* Residue conservation analysis
PDB id:
1dik
Name: Phosphotransferase
Title: Pyruvate phosphate dikinase
Structure: Pyruvate phosphate dikinase. Chain: a. Synonym: ppdk. Engineered: yes. Other_details: ph7.0, crystallization at 30c, data collecti temp
Source: Clostridium symbiosum. Organism_taxid: 1512. Gene: ppdk. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.182    
Authors: O.Herzberg,C.C.H.Chen
Key ref: O.Herzberg et al. (1996). Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc Natl Acad Sci U S A, 93, 2652-2657. PubMed id: 8610096
Date:
06-Dec-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22983  (PPDK_CLOSY) -  Pyruvate, phosphate dikinase
Seq:
Struc:
 
Seq:
Struc:
874 a.a.
869 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.9.1  - Pyruvate, phosphate dikinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
ATP
+ pyruvate
+ phosphate
= AMP
+ phosphoenolpyruvate
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 93:2652-2657 (1996)
PubMed id: 8610096  
 
 
Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.
O.Herzberg, C.C.Chen, G.Kapadia, M.McGuire, L.J.Carroll, S.J.Noh, D.Dunaway-Mariano.
 
  ABSTRACT  
 
The crystal structure of pyruvate phosphate dikinase, a histidyl multiphosphotransfer enzyme that synthesizes adenosine triphosphate, reveals a three-domain molecule in which the phosphohistidine domain is flanked by the nucleotide and the phosphoenolpyruvate/pyruvate domains, with the two substrate binding sites approximately 45 angstroms apart. The modes of substrate binding have been deduced by analogy to D-Ala-D-Ala ligase and to pyruvate kinase. Coupling between the two remote active sites is facilitated by two conformational states of the phosphohistidine domain. While the crystal structure represents the state of interaction with the nucleotide, the second state is achieved by swiveling around two flexible peptide linkers. This dramatic conformational transition brings the phosphocarrier residue in close proximity to phosphoenolpyruvate/pyruvate. The swiveling-domain paradigm provides an effective mechanism for communication in complex multidomain/multiactive site proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19801641 A.E.Oberholzer, P.Schneider, C.Siebold, U.Baumann, and B.Erni (2009).
Crystal structure of enzyme I of the phosphoenolpyruvate sugar phosphotransferase system in the dephosphorylated state.
  J Biol Chem, 284, 33169-33176.
PDB code: 2wqd
18511452 K.Suzuki, S.Ito, A.Shimizu-Ibuka, and H.Sakai (2008).
Crystal structure of pyruvate kinase from Geobacillus stearothermophilus.
  J Biochem, 144, 305-312.
PDB code: 2e28
17710553 P.Stephen, R.Vijayan, A.Bhat, N.Subbarao, and R.N.Bamezai (2008).
Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.
  J Comput Aided Mol Des, 22, 647-660.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17299750 I.Kufareva, L.Budagyan, E.Raush, M.Totrov, and R.Abagyan (2007).
PIER: protein interface recognition for structural proteomics.
  Proteins, 67, 400-417.  
17053069 A.Teplyakov, K.Lim, P.P.Zhu, G.Kapadia, C.C.Chen, J.Schwartz, A.Howard, P.T.Reddy, A.Peterkofsky, and O.Herzberg (2006).
Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein.
  Proc Natl Acad Sci U S A, 103, 16218-16223.
PDB code: 2hwg
17158705 J.Deutscher, C.Francke, and P.W.Postma (2006).
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
  Microbiol Mol Biol Rev, 70, 939.  
16915520 K.Parsley, and J.M.Hibberd (2006).
The Arabidopsis PPDK gene is transcribed from two promoters to produce differentially expressed transcripts responsible for cytosolic and plastidic proteins.
  Plant Mol Biol, 62, 339-349.  
15853884 N.R.Williamson, H.T.Simonsen, R.A.Ahmed, G.Goldet, H.Slater, L.Woodley, F.J.Leeper, and G.P.Salmond (2005).
Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces.
  Mol Microbiol, 56, 971-989.  
15547277 S.Schmeling, A.Narmandakh, O.Schmitt, N.Gad'on, K.Schühle, and G.Fuchs (2004).
Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica.
  J Bacteriol, 186, 8044-8057.  
14675542 C.V.Smith, and J.C.Sacchettini (2003).
Mycobacterium tuberculosis: a model system for structural genomics.
  Curr Opin Struct Biol, 13, 658-664.  
12517345 D.I.Liao, L.Reiss, I.Turner, and G.Dotson (2003).
Structure of glycerol dehydratase reactivase: a new type of molecular chaperone.
  Structure, 11, 109-119.
PDB code: 1nbw
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
12837779 J.M.Johnston, V.L.Arcus, C.J.Morton, M.W.Parker, and E.N.Baker (2003).
Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis.
  J Bacteriol, 185, 4057-4065.
PDB code: 1nxj
14568143 K.S.Makarova, and E.V.Koonin (2003).
Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.
  FEMS Microbiol Lett, 227, 17-23.  
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
11514230 A.M.Cerdeño, M.J.Bibb, and G.L.Challis (2001).
Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes.
  Chem Biol, 8, 817-829.  
11371194 O.Asojo, J.Friedman, N.Adir, V.Belakhov, Y.Shoham, and T.Baasov (2001).
Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
  Biochemistry, 40, 6326-6334.
PDB codes: 1g7u 1g7v
10715138 B.R.Howard, J.A.Endrizzi, and S.J.Remington (2000).
Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 A resolution: mechanistic implications.
  Biochemistry, 39, 3156-3168.
PDB code: 1d8c
10969019 H.Kikuchi, H.Wako, K.Yura, M.Go, and M.Mimuro (2000).
Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis.
  Biophys J, 79, 1587-1600.  
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
11092947 L.W.Cosenza, F.Bringaud, T.Baltz, and F.M.Vellieux (2000).
Crystallization and preliminary crystallographic investigation of glycosomal pyruvate phosphate dikinase from Trypanosoma brucei.
  Acta Crystallogr D Biol Crystallogr, 56, 1688-1690.  
10736161 S.J.Brokx, J.Talbot, F.Georges, and E.B.Waygood (2000).
Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system. In vitro intragenic complementation: the roles of Arg126 in phosphoryl transfer and the C-terminal domain in dimerization.
  Biochemistry, 39, 3624-3635.  
10029528 J.B.Thoden, G.Wesenberg, F.M.Raushel, and H.M.Holden (1999).
Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
  Biochemistry, 38, 2347-2357.
PDB code: 1bxr
10569929 P.P.Zhu, R.H.Szczepanowski, N.J.Nosworthy, A.Ginsburg, and A.Peterkofsky (1999).
Reconstitution studies using the helical and carboxy-terminal domains of enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system.
  Biochemistry, 38, 15470-15479.  
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9507062 E.Saavedra-Lira, L.Ramirez-Silva, and R.Perez-Montfort (1998).
Expression and characterization of recombinant pyruvate phosphate dikinase from Entamoeba histolytica.
  Biochim Biophys Acta, 1382, 47-54.  
  10082373 K.A.Denessiouk, J.V.Lehtonen, and M.S.Johnson (1998).
Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition.
  Protein Sci, 7, 1768-1771.  
  9605318 K.A.Denessiouk, J.V.Lehtonen, T.Korpela, and M.S.Johnson (1998).
Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites.
  Protein Sci, 7, 1136-1146.  
9463376 L.Esser, C.R.Wang, M.Hosaka, C.S.Smagula, T.C.Südhof, and J.Deisenhofer (1998).
Synapsin I is structurally similar to ATP-utilizing enzymes.
  EMBO J, 17, 977-984.
PDB codes: 1auv 1aux
9843369 W.Wang, T.J.Kappock, J.Stubbe, and S.E.Ealick (1998).
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
  Biochemistry, 37, 15647-15662.
PDB code: 1gso
9108017 A.M.Buckle, R.Zahn, and A.R.Fersht (1997).
A structural model for GroEL-polypeptide recognition.
  Proc Natl Acad Sci U S A, 94, 3571-3575.
PDB code: 1kid
9054557 D.S.Garrett, Y.J.Seok, D.I.Liao, A.Peterkofsky, A.M.Gronenborn, and G.M.Clore (1997).
Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR.
  Biochemistry, 36, 2517-2530.
PDB codes: 1eza 1ezb 1ezc 1ezd
9204285 J.Heringa, and W.R.Taylor (1997).
Three-dimensional domain duplication, swapping and stealing.
  Curr Opin Struct Biol, 7, 416-421.  
9204284 J.Reizer, and M.H.Saier (1997).
Modular multidomain phosphoryl transfer proteins of bacteria.
  Curr Opin Struct Biol, 7, 407-415.  
  9416615 M.Y.Galperin, and E.V.Koonin (1997).
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
  Protein Sci, 6, 2639-2643.  
8804825 A.G.Murzin (1996).
Structural classification of proteins: new superfamilies.
  Curr Opin Struct Biol, 6, 386-394.  
8805571 D.I.Liao, E.Silverton, Y.J.Seok, B.R.Lee, A.Peterkofsky, and D.R.Davies (1996).
The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.
  Structure, 4, 861-872.
PDB code: 1zym
8679615 M.McGuire, L.J.Carroll, L.Yankie, S.H.Thrall, D.Dunaway-Mariano, O.Herzberg, B.Jayaram, and B.H.Haley (1996).
Determination of the nucleotide binding site within Clostridium symbiosum pyruvate phosphate dikinase by photoaffinity labeling, site-directed mutagenesis, and structural analysis.
  Biochemistry, 35, 8544-8552.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.