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PDBsum entry 4brk

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
4brk
Jmol
Contents
Protein chains
359 a.a.
Ligands
UNP ×2
MES ×2
GOL ×2
Metals
_CL ×3
_MG ×2
Waters ×771
PDB id:
4brk
Name: Hydrolase
Title: Legionella pneumophila ntpdase1 n302y variant crystal form iii (closed) in complex with mg umppnp
Structure: Ectonucleoside triphosphate diphosphohydrolase i. Chain: a, b. Fragment: residues 35-393. Synonym: ntpdase1. Engineered: yes. Mutation: yes
Source: Legionella pneumophila. Organism_taxid: 446. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.129     R-free:   0.177
Authors: M.Zebisch,P.Schaefer,P.Lauble,N.Straeter
Key ref: M.Zebisch et al. (2013). Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases. Structure, 21, 1460-1475. PubMed id: 23830739 DOI: 10.1016/j.str.2013.05.016
Date:
04-Jun-13     Release date:   17-Jul-13    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5ZUA2  (Q5ZUA2_LEGPH) -  Ectonucleoside triphosphate diphosphohydrolase I
Seq:
Struc:
393 a.a.
359 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/j.str.2013.05.016 Structure 21:1460-1475 (2013)
PubMed id: 23830739  
 
 
Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases.
M.Zebisch, M.Krauss, P.Schäfer, P.Lauble, N.Sträter.
 
  ABSTRACT  
 
In vertebrates, membrane-bound ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) on the cell surface are responsible for signal conversion and termination in purinergic signaling by extracellular nucleotides. Here we present apo and complex structures of the rat NTPDase2 extracellular domain and Legionella pneumophila NTPDase1, including a high-resolution structure with a transition-state analog. Comparison of ATP and ADP binding modes shows how NTPDases engage the same catalytic site for hydrolysis of nucleoside triphosphates and diphosphates. We find that this dual specificity is achieved at the expense of base specificity. Structural and mutational studies indicate that a conserved active-site water is replaced by the phosphate product immediately after phosphoryl transfer. Partial base specificity for purines in LpNTPDase1 is based on a different intersubunit base binding site for pyrimidine bases. A comparison of the bacterial enzyme in six independent crystal forms shows that NTPDases can undergo a domain closure motion of at least 17°.