PDBsum entry 1t6c

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protein ligands metals links
Hydrolase PDB id
Protein chain
306 a.a. *
MPD ×6
_CL ×3
Waters ×390
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structural characterization of the ppx/gppa protein family: structure of the aquifex aeolicus family member
Structure: Exopolyphosphatase. Chain: a. Synonym: ppx/gppa phosphatase. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. Gene: ppx. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.53Å     R-factor:   0.162     R-free:   0.217
Authors: O.Kristensen,M.Laurberg,A.Liljas,J.S.Kastrup,M.Gajhede
Key ref:
O.Kristensen et al. (2004). Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry, 43, 8894-8900. PubMed id: 15248747 DOI: 10.1021/bi049083c
06-May-04     Release date:   03-Aug-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O67040  (O67040_AQUAE) -  Exopolyphosphatase
312 a.a.
306 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1021/bi049083c Biochemistry 43:8894-8900 (2004)
PubMed id: 15248747  
Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family.
O.Kristensen, M.Laurberg, A.Liljas, J.S.Kastrup, M.Gajhede.
Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the PPX/GPPA family. The protein has a two-domain structure with an active site located in the interdomain cleft. Two crystal forms were investigated (type I and II) at resolutions of 1.53 and 2.15 A, respectively. This revealed a structural flexibility that has previously been described as a "butterfly-like" cleft opening around the active site in other actin-like superfamily proteins. A calcium ion is observed at the center of this region in type I crystals, substantiating that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21484095 A.F.Knowles (2011).
The GDA1_CD39 superfamily: NTPDases with diverse functions.
  Purinergic Signal, 7, 21-45.  
20159467 J.P.Vivian, P.Riedmaier, H.Ge, J.Le Nours, F.M.Sansom, M.C.Wilce, E.Byres, M.Dias, J.W.Schmidberger, P.J.Cowan, A.J.d'Apice, E.L.Hartland, J.Rossjohn, and T.Beddoe (2010).
Crystal structure of a Legionella pneumophila ecto -triphosphate diphosphohydrolase, a structural and functional homolog of the eukaryotic NTPDases.
  Structure, 18, 228-238.
PDB codes: 3aap 3aaq 3aar
19344251 N.N.Rao, M.R.Gómez-García, and A.Kornberg (2009).
Inorganic polyphosphate: essential for growth and survival.
  Annu Rev Biochem, 78, 605-647.  
18458329 M.Zebisch, and N.Sträter (2008).
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling.
  Proc Natl Acad Sci U S A, 105, 6882-6887.
PDB codes: 3cj1 3cj7 3cj9 3cja
17827150 J.Fang, F.A.Ruiz, M.Docampo, S.Luo, J.C.Rodrigues, L.S.Motta, P.Rohloff, and R.Docampo (2007).
Overexpression of a Zn2+-sensitive soluble exopolyphosphatase from Trypanosoma cruzi depletes polyphosphate and affects osmoregulation.
  J Biol Chem, 282, 32501-32510.  
17215253 M.Tammenkoski, V.M.Moiseev, M.Lahti, E.Ugochukwu, T.H.Brondijk, S.A.White, R.Lahti, and A.A.Baykov (2007).
Kinetic and mutational analyses of the major cytosolic exopolyphosphatase from Saccharomyces cerevisiae.
  J Biol Chem, 282, 9302-9311.  
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
  17710224 T.L.Kirley, P.A.Crawford, and T.M.Smith (2006).
The structure of the nucleoside triphosphate diphosphohydrolases (NTPDases) as revealed by mutagenic and computational modeling analyses.
  Purinergic Signal, 2, 379-389.  
16771627 Z.Liu, and R.A.Butow (2006).
Mitochondrial retrograde signaling.
  Annu Rev Genet, 40, 159-185.  
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