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PDBsum entry 1ihu

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protein ligands metals links
Hydrolase PDB id
1ihu
Jmol
Contents
Protein chain
540 a.a. *
Ligands
ADP
ADP-AF3
TAS
Metals
_MG ×2
_CD ×8
_CL ×3
Waters ×192
* Residue conservation analysis
PDB id:
1ihu
Name: Hydrolase
Title: Crystal structure of the escherichia coli arsenite-transloca atpase in complex with mg-adp-alf3
Structure: Arsenical pump-driving atpase. Chain: a. Synonym: arsenite-translocating atpase, arsenical resistanc engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: arsa. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.15Å     R-factor:   0.215     R-free:   0.262
Authors: T.Zhou,S.Radaev,B.P.Rosen,D.L.Gatti
Key ref:
T.Zhou et al. (2001). Conformational changes in four regions of the Escherichia coli ArsA ATPase link ATP hydrolysis to ion translocation. J Biol Chem, 276, 30414-30422. PubMed id: 11395509 DOI: 10.1074/jbc.M103671200
Date:
20-Apr-01     Release date:   12-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08690  (ARSA1_ECOLX) -  Arsenical pump-driving ATPase
Seq:
Struc:
 
Seq:
Struc:
583 a.a.
540 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.6.3.16  - Arsenite-transporting ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + arsenite(In) = ADP + phosphate + arsenite(Out)
ATP
+ H(2)O
+ arsenite(In)
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
+ arsenite(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M103671200 J Biol Chem 276:30414-30422 (2001)
PubMed id: 11395509  
 
 
Conformational changes in four regions of the Escherichia coli ArsA ATPase link ATP hydrolysis to ion translocation.
T.Zhou, S.Radaev, B.P.Rosen, D.L.Gatti.
 
  ABSTRACT  
 
Structures of ArsA with ATP, AMP-PNP, or ADP.AlF(3) bound at the A2 nucleotide binding site were determined. Binding of different nucleotides modifies the coordination sphere of Mg(2+). In particular, the changes elicited by ADP.AlF(3) provide insights into the mechanism of ATP hydrolysis. In-line attack by water onto the gamma-phosphate of ATP would be followed first by formation of a trigonal intermediate and then by breaking of the scissile bond between the beta- and gamma-phosphates. Motions of amino acid side chains at the A2 nucleotide binding site during ATP binding and hydrolysis propagate at a distance, producing conformational changes in four different regions of the protein corresponding to helices H4-H5, helices H9-H10, helices H13-H15, and to the S1-H2-S2 region. These elements are extensions of, respectively, the Switch I and Switch II regions, the A-loop (a small loop near the nucleotide adenine moiety), and the P-loop. Based on the observed conformational changes, it is proposed that ArsA functions as a reciprocating engine that hydrolyzes 2 mol of ATP per each cycle of ion translocation across the membrane.
 
  Selected figure(s)  
 
Figure 7.
Fig. 7. ArsA functional domains. Center panel, the molecular surface of A1 is dissected into four regions whose conformational changes are under control of the P-loop (green), the Switch I region (pink), the Switch II region (cyan), and the A-Loop (red). ADP bound at the A1 NBS is shown as bonds colored according to atom types; Mg2+ and As/Sb(III) are shown as CPK in magenta and purple-blue, respectively. Corner panels, C traces of the domains whose surface is shown in the center panel. Mg2+-ADP is shown for reference next to each trace. Side chains are shown with yellow bonds; Mg2+ and As/Sb(III) as CPK in magenta and purple-blue, respectively.
Figure 8.
Fig. 8. ArsA catalytic cycle. Helices H9-H10 of A1 (red) and A2 (cyan) are the arms of a gate alternating in the "open" and "closed" positions. An As(III) ion is shown as a blue sphere. For each cycle of ion translocation, one ATP is used at the A2 NBS in the transfer step, and one at the A1 NBS in the re-isomerization step. Although the scheme depicts a hypothetical situation in which only one As(III) ion is translocated per catalytic cycle, the actual stoichiometry of ions translocated per ATP hydrolyzed is not known.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 30414-30422) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21188475 A.Abdul Ajees, J.Yang, and B.P.Rosen (2011).
The ArsD As(III) metallochaperone.
  Biometals, 24, 391-399.  
20361763 J.Yang, S.Rawat, T.L.Stemmler, and B.P.Rosen (2010).
Arsenic binding and transfer by the ArsD As(III) metallochaperone.
  Biochemistry, 49, 3658-3666.  
19675567 A.Mateja, A.Szlachcic, M.E.Downing, M.Dobosz, M.Mariappan, R.S.Hegde, and R.J.Keenan (2009).
The structural basis of tail-anchored membrane protein recognition by Get3.
  Nature, 461, 361-366.
PDB codes: 2woj 2woo
19706470 C.J.Suloway, J.W.Chartron, M.Zaslaver, and W.M.Clemons (2009).
Model for eukaryotic tail-anchored protein binding based on the structure of Get3.
  Proc Natl Acad Sci U S A, 106, 14849-14854.
PDB codes: 3ibg 3idq
19525115 D.C.Lee, and Z.Jia (2009).
Emerging structural insights into bacterial tyrosine kinases.
  Trends Biochem Sci, 34, 351-357.  
19948960 G.Bozkurt, G.Stjepanovic, F.Vilardi, S.Amlacher, K.Wild, G.Bange, V.Favaloro, K.Rippe, E.Hurt, B.Dobberstein, and I.Sinning (2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
  Proc Natl Acad Sci U S A, 106, 21131-21136.
PDB codes: 3iqw 3iqx
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
17151076 C.G.Noble, B.Beuth, and I.A.Taylor (2007).
Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.
  Nucleic Acids Res, 35, 87-99.
PDB code: 2npi
17148509 R.Thilakaraj, K.Raghunathan, S.Anishetty, and G.Pennathur (2007).
In silico identification of putative metal binding motifs.
  Bioinformatics, 23, 267-271.  
17955352 Y.F.Lin, J.Yang, and B.P.Rosen (2007).
ArsD: an As(III) metallochaperone for the ArsAB As(III)-translocating ATPase.
  J Bioenerg Biomembr, 39, 453-458.  
12675792 J.Lutkenhaus, and M.Sundaramoorthy (2003).
MinD and role of the deviant Walker A motif, dimerization and membrane binding in oscillation.
  Mol Microbiol, 48, 295-303.  
12777806 P.Retailleau, and T.Prangé (2003).
Phasing power at the K absorption edge of organic arsenic.
  Acta Crystallogr D Biol Crystallogr, 59, 887-896.
PDB code: 1n4f
11844750 A.L.Davidson (2002).
Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters.
  J Bacteriol, 184, 1225-1233.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
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.