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PDBsum entry 1t6c

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protein ligands metals links
Hydrolase PDB id
1t6c
Jmol
Contents
Protein chain
306 a.a. *
Ligands
MPD ×6
Metals
IOD
_CA
_CL ×3
Waters ×390
* Residue conservation analysis
PDB id:
1t6c
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.
Resolution:
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
Date:
06-May-04     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O67040  (O67040_AQUAE) -  Exopolyphosphatase
Seq:
Struc:
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.
 
  ABSTRACT  
 
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.  
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 codes are shown on the right.