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PDBsum entry 1aq2

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protein ligands metals links
Kinase PDB id
1aq2
Jmol PyMol
Contents
Protein chain
534 a.a. *
Ligands
ATP
PYR
Metals
_MN
_MG
Waters ×232
* Residue conservation analysis
PDB id:
1aq2
Name: Kinase
Title: Phosphoenolpyruvate carboxykinase
Structure: Phosphoenolpyruvate carboxykinase. Chain: a. Synonym: atp-oxaloacetate carboxy-lyase (atp). Engineered: yes. Other_details: ordered magnesium and manganese ions observe atp
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: native promoter of e. Coli pcka gene, highly growth to early stationary phase in the absence of carbohyd
Resolution:
1.90Å     R-factor:   0.218     R-free:   0.260
Authors: L.W.Tari,A.Matte,H.Goldie,L.T.J.Delbaere
Key ref: L.W.Tari et al. (1997). Mg(2+)-Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions. Nat Struct Biol, 4, 990-994. PubMed id: 9406547
Date:
05-Aug-97     Release date:   14-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22259  (PCKA_ECOLI) -  Phosphoenolpyruvate carboxykinase [ATP]
Seq:
Struc:
 
Seq:
Struc:
540 a.a.
534 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.49  - Phosphoenolpyruvate carboxykinase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+
oxaloacetate
Bound ligand (Het Group name = PYR)
matches with 66.67% similarity
= ADP
+ phosphoenolpyruvate
+ CO(2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
    reference    
 
 
Nat Struct Biol 4:990-994 (1997)
PubMed id: 9406547  
 
 
Mg(2+)-Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions.
L.W.Tari, A.Matte, H.Goldie, L.T.Delbaere.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20524049 E.Pérez, and E.Cardemil (2010).
Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: the relevance of Glu299 and Leu460 for nucleotide binding.
  Protein J, 29, 299-305.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
19638345 G.M.Carlson, and T.Holyoak (2009).
Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis.
  J Biol Chem, 284, 27037-27041.  
19021757 L.Dharmarajan, C.L.Case, P.Dunten, and B.Mukhopadhyay (2008).
Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate.
  FEBS J, 275, 5810-5819.  
18385384 L.Xie, and P.E.Bourne (2008).
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
  Proc Natl Acad Sci U S A, 105, 5441-5446.  
17195942 A.Yévenes, F.D.González-Nilo, and E.Cardemil (2007).
Relevance of phenylalanine 216 in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn(II).
  Protein J, 26, 135-141.  
17164532 T.C.Terwilliger, P.D.Adams, N.W.Moriarty, and J.D.Cohn (2007).
Ligand identification using electron-density map correlations.
  Acta Crystallogr D Biol Crystallogr, 63, 101-107.  
16788205 K.I.Varughese, I.Tsigelny, and H.Zhao (2006).
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state.
  J Bacteriol, 188, 4970-4977.
PDB code: 2ftk
  16741238 M.V.Lasker, S.M.Kuruvilla, M.M.Gajjar, A.Kapoor, and S.K.Nair (2006).
Metal ion-mediated reduction in surface entropy improves diffraction quality of crystals of the IRAK-4 death domain.
  J Biomol Tech, 17, 114-121.  
15720564 F.Bengs, A.Scholz, D.Kuhn, and M.Wiese (2005).
LmxMPK9, a mitogen-activated protein kinase homologue affects flagellar length in Leishmania mexicana.
  Mol Microbiol, 55, 1606-1615.  
16239727 M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, and N.Kunishima (2005).
Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
  Acta Crystallogr D Biol Crystallogr, 61, 1500-1507.
PDB codes: 1j3b 1xkv
15983413 Y.A.Leduc, L.Prasad, M.Laivenieks, J.G.Zeikus, and L.T.Delbaere (2005).
Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif.
  Acta Crystallogr D Biol Crystallogr, 61, 903-912.
PDB codes: 1ygg 1ylh
15006638 C.Bueno, F.D.González-Nilo, M.Victoria Encinas, and E.Cardemil (2004).
Substrate binding to fluorescent labeled wild type, Lys213Arg, and HIS233Gln Saccharomyces cerevisiae phosphoenolpyruvate carboxykinases.
  Int J Biochem Cell Biol, 36, 861-869.  
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.  
15231795 W.Fukuda, T.Fukui, H.Atomi, and T.Imanaka (2004).
First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  J Bacteriol, 186, 4620-4627.  
12837799 A.Sudom, R.Walters, L.Pastushok, D.Goldie, L.Prasad, L.T.Delbaere, and H.Goldie (2003).
Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin.
  J Bacteriol, 185, 4233-4242.
PDB code: 1os1
12784360 E.J.Gardiner, P.Willett, and P.J.Artymiuk (2003).
GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1.
  Proteins, 52, 10-14.  
14506262 K.A.Pattridge, C.H.Weber, J.A.Friesen, S.Sanker, C.Kent, and M.L.Ludwig (2003).
Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis.
  J Biol Chem, 278, 51863-51871.
PDB code: 1n1d
12837773 S.Nessler, S.Fieulaine, S.Poncet, A.Galinier, J.Deutscher, and J.Janin (2003).
HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in Gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate.
  J Bacteriol, 185, 4003-4010.  
11796714 A.Galinier, J.P.Lavergne, C.Geourjon, S.Fieulaine, S.Nessler, and J.M.Jault (2002).
A new family of phosphotransferases with a P-loop motif.
  J Biol Chem, 277, 11362-11367.  
12383254 M.V.Encinas, F.D.González-Nilo, H.Goldie, and E.Cardemil (2002).
Ligand interactions and protein conformational changes of phosphopyridoxyl-labeled Escherichia coli phosphoenolpyruvate carboxykinase determined by fluorescence spectroscopy.
  Eur J Biochem, 269, 4960-4968.  
12359875 S.Fieulaine, S.Morera, S.Poncet, I.Mijakovic, A.Galinier, J.Janin, J.Deutscher, and S.Nessler (2002).
X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr.
  Proc Natl Acad Sci U S A, 99, 13437-13441.
PDB codes: 1kkl 1kkm
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9576910 H.Käck, K.J.Gibson, Y.Lindqvist, and G.Schneider (1998).
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
  Proc Natl Acad Sci U S A, 95, 5495-5500.
PDB codes: 1a82 1dak
9920388 L.Carrasco, F.D.González, and E.Cardemil (1998).
Interaction of adenosine nucleotide analogs with Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase.
  Biochim Biophys Acta, 1429, 93.  
9860824 P.J.Focia, S.P.Craig, and A.E.Eakin (1998).
Approaching the transition state in the crystal structure of a phosphoribosyltransferase.
  Biochemistry, 37, 17120-17127.
PDB code: 1tc2
9914251 S.Doublié, and T.Ellenberger (1998).
The mechanism of action of T7 DNA polymerase.
  Curr Opin Struct Biol, 8, 704-712.  
9572839 T.M.Larsen, M.M.Benning, I.Rayment, and G.H.Reed (1998).
Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel.
  Biochemistry, 37, 6247-6255.
PDB codes: 1a49 1a5u
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.

 

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