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PDBsum entry 1g99

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1g99
Jmol
Contents
Protein chains
398 a.a. *
Ligands
SO4 ×2
ADP ×2
Waters ×158
* Residue conservation analysis
PDB id:
1g99
Name: Transferase
Title: An ancient enzyme: acetate kinase from methanosarcina thermophila
Structure: Acetate kinase. Chain: a, b. Engineered: yes
Source: Methanosarcina thermophila. Organism_taxid: 2210. Gene: ack. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.147     R-free:   0.188
Authors: K.A.Buss,D.R.Cooper,C.Ingram-Smith,J.G.Ferry,D.A.Sanders, M.S.Hasson
Key ref: K.A.Buss et al. (2001). Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J Bacteriol, 183, 680-686. PubMed id: 11133963
Date:
22-Nov-00     Release date:   27-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38502  (ACKA_METTE) -  Acetate kinase
Seq:
Struc:
408 a.a.
398 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.2.1  - Acetate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + acetate = ADP + acetyl phosphate
ATP
+ acetate
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ acetyl phosphate
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
J Bacteriol 183:680-686 (2001)
PubMed id: 11133963  
 
 
Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases.
K.A.Buss, D.R.Cooper, C.Ingram-Smith, J.G.Ferry, D.A.Sanders, M.S.Hasson.
 
  ABSTRACT  
 
Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the alpha-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20528692 J.G.Ferry (2010).
How to make a living by exhaling methane.
  Annu Rev Microbiol, 64, 453-473.  
20146278 J.Kim, A.J.Pierik, and W.Buckel (2010).
A complex of 2-hydroxyisocaproyl-coenzyme A dehydratase and its activator from Clostridium difficile stabilized by aluminium tetrafluoride-adenosine diphosphate.
  Chemphyschem, 11, 1307-1312.  
20048057 M.Julotok, A.K.Singh, C.Gatto, and B.J.Wilkinson (2010).
Influence of fatty acid precursors, including food preservatives, on the growth and fatty acid composition of Listeria monocytogenes at 37 and 10degreesC.
  Appl Environ Microbiol, 76, 1423-1432.  
19274093 D.Y.Little, and L.Chen (2009).
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
  PLoS ONE, 4, e4762.  
19201797 J.Diao, and M.S.Hasson (2009).
Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases.
  J Bacteriol, 191, 2521-2529.
PDB code: 1saz
19172740 A.Hecker, R.Lopreiato, M.Graille, B.Collinet, P.Forterre, D.Libri, and H.van Tilbeurgh (2008).
Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex.
  EMBO J, 27, 2340-2351.
PDB code: 2vwb
18378593 J.G.Ferry, and D.J.Lessner (2008).
Methanogenesis in marine sediments.
  Ann N Y Acad Sci, 1125, 147-157.  
18294673 S.Mukhopadhyay, M.S.Hasson, and D.A.Sanders (2008).
A continuous assay of acetate kinase activity: measurement of inorganic phosphate release generated by hydroxylaminolysis of acetyl phosphate.
  Bioorg Chem, 36, 65-69.  
17999468 A.Gorrell, and J.G.Ferry (2007).
Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching.
  Biochemistry, 46, 14170-14176.  
17766251 A.Hecker, N.Leulliot, D.Gadelle, M.Graille, A.Justome, P.Dorlet, C.Brochier, S.Quevillon-Cheruel, E.Le Cam, H.van Tilbeurgh, and P.Forterre (2007).
An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro.
  Nucleic Acids Res, 35, 6042-6051.
PDB codes: 2ivn 2ivo 2ivp
17873883 A.Orlova, E.C.Garner, V.E.Galkin, J.Heuser, R.D.Mullins, and E.H.Egelman (2007).
The structure of bacterial ParM filaments.
  Nat Struct Mol Biol, 14, 921-926.
PDB code: 2qu4
17954980 D.K.Simanshu, S.Chittori, H.S.Savithri, and M.R.Murthy (2007).
Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate.
  J Biosci, 32, 1195-1206.  
16905100 J.Alvarado, A.Ghosh, T.Janovitz, A.Jauregui, M.S.Hasson, and D.A.Sanders (2006).
Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.
  Structure, 14, 1263-1272.
PDB code: 1u6z
16855243 K.Yang, Y.Eyobo, L.A.Brand, D.Martynowski, D.Tomchick, E.Strauss, and H.Zhang (2006).
Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria.
  J Bacteriol, 188, 5532-5540.
PDB code: 2gtd
16496142 T.Shigematsu, S.Era, Y.Mizuno, K.Ninomiya, Y.Kamegawa, S.Morimura, and K.Kida (2006).
Microbial community of a mesophilic propionate-degrading methanogenic consortium in chemostat cultivation analyzed based on 16S rRNA and acetate kinase genes.
  Appl Microbiol Biotechnol, 72, 401-415.  
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
15755952 A.J.Wolfe (2005).
The acetate switch.
  Microbiol Mol Biol Rev, 69, 12-50.  
15774882 C.Ingram-Smith, A.Gorrell, S.H.Lawrence, P.Iyer, K.Smith, and J.G.Ferry (2005).
Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase.
  J Bacteriol, 187, 2386-2394.  
  16508089 D.K.Simanshu, and M.R.Murthy (2005).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 52-55.  
16218867 W.Buckel, B.M.Martins, A.Messerschmidt, and B.T.Golding (2005).
Radical-mediated dehydration reactions in anaerobic bacteria.
  Biol Chem, 386, 951-959.  
  15374661 J.Kim, M.Hetzel, C.D.Boiangiu, and W.Buckel (2004).
Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria.
  FEMS Microbiol Rev, 28, 455-468.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
15062079 P.P.Iyer, S.H.Lawrence, K.B.Luther, K.R.Rajashankar, H.P.Yennawar, J.G.Ferry, and H.Schindelin (2004).
Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila.
  Structure, 12, 559-567.
PDB code: 1qzt
15466045 V.V.Lunin, Y.Li, J.D.Schrag, P.Iannuzzi, M.Cygler, and A.Matte (2004).
Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose.
  J Bacteriol, 186, 6915-6927.
PDB codes: 1q18 1sz2
12520055 J.Chen, J.B.Anderson, C.DeWeese-Scott, N.D.Fedorova, L.Y.Geer, S.He, D.I.Hurwitz, J.D.Jackson, A.R.Jacobs, C.J.Lanczycki, C.A.Liebert, C.Liu, T.Madej, A.Marchler-Bauer, G.H.Marchler, R.Mazumder, A.N.Nikolskaya, B.S.Rao, A.R.Panchenko, B.A.Shoemaker, V.Simonyan, J.S.Song, P.A.Thiessen, S.Vasudevan, Y.Wang, R.A.Yamashita, J.J.Yin, and S.H.Bryant (2003).
MMDB: Entrez's 3D-structure database.
  Nucleic Acids Res, 31, 474-477.  
12777787 J.Diao, D.R.Cooper, D.A.Sanders, and M.S.Hasson (2003).
Crystallization of butyrate kinase 2 from Thermotoga maritima mediated by vapor diffusion of acetic acid.
  Acta Crystallogr D Biol Crystallogr, 59, 1100-1102.  
12005432 S.Ramón-Maiques, A.Marina, F.Gil-Ortiz, I.Fita, and V.Rubio (2002).
Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis.
  Structure, 10, 329-342.
PDB codes: 1gs5 1gsj
11698658 M.Unciuleac, and M.Boll (2001).
Mechanism of ATP-driven electron transfer catalyzed by the benzene ring-reducing enzyme benzoyl-CoA reductase.
  Proc Natl Acad Sci U S A, 98, 13619-13624.  
11737196 U.M.Kohlstock, K.P.Rücknagel, M.Reuter, A.Schierhorn, J.R.Andreesen, and B.Söhling (2001).
Cys359 of GrdD is the active-site thiol that catalyses the final step of acetyl phosphate formation by glycine reductase from Eubacterium acidaminophilum.
  Eur J Biochem, 268, 6417-6425.  
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.