PDBsum entry 1wje

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protein metals Protein-protein interface(s) links
Zn-binding protein PDB id
Protein chains
46 a.a. *
_CD ×2
* Residue conservation analysis
PDB id:
Name: Zn-binding protein
Title: Solution structure of h12c mutant of the n-terminal zn binding domain of HIV-1 integrase complexed to cadmium, nmr, minimized average structure
Structure: HIV-1 integrase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Human immunodeficiency virus 1. Organism_taxid: 11676. Cell_line: bl21. Gene: potential. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: M.Cai,A.M.Gronenborn,G.M.Clore
Key ref: M.Cai et al. (1998). Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium. Protein Sci, 7, 2669-2674. PubMed id: 9865962 DOI: 10.1002/pro.5560071221
11-Jun-98     Release date:   16-Dec-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04587  (POL_HV1B5) -  Gag-Pol polyprotein
1447 a.a.
46 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.  - RNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
   Enzyme class 2: E.C.  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
   Enzyme class 3: E.C.  - Exoribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
   Enzyme class 4: E.C.  - Retroviral ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 5: E.C.  - HIV-1 retropepsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     zinc ion binding     1 term  


DOI no: 10.1002/pro.5560071221 Protein Sci 7:2669-2674 (1998)
PubMed id: 9865962  
Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.
M.Cai, Y.Huang, M.Caffrey, R.Zheng, R.Craigie, G.M.Clore, A.M.Gronenborn.
The solution structure of His12 --> Cys mutant of the N-terminal zinc binding domain (residues 1-55; IN(1-55)) of HIV-1 integrase complexed to cadmium has been solved by multidimensional heteronuclear NMR spectroscopy. The overall structure is very similar to that of the wild-type N-terminal domain complexed to zinc. In contrast to the wild-type domain, however, which exists in two interconverting conformational states arising from different modes of coordination of the two histidine side chains to the metal, the cadmium complex of the His12 --> Cys mutant exists in only a single form at low pH. The conformation of the polypeptide chain encompassing residues 10-18 is intermediate between the two forms of the wild-type complex.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21275045 L.Q.Al-Mawsawi, and N.Neamati (2011).
Allosteric Inhibitor Development Targeting HIV-1 Integrase.
  ChemMedChem, 6, 228-241.  
19490099 M.Jaskolski, J.N.Alexandratos, G.Bujacz, and A.Wlodawer (2009).
Piecing together the structure of retroviral integrase, an important target in AIDS therapy.
  FEBS J, 276, 2926-2946.  
19544345 M.L.Barreca, N.Iraci, L.De Luca, and A.Chimirri (2009).
Induced-fit docking approach provides insight into the binding mode and mechanism of action of HIV-1 integrase inhibitors.
  ChemMedChem, 4, 1446-1456.  
19229934 O.Iranzo, T.Jakusch, K.H.Lee, L.Hemmingsen, and V.L.Pecoraro (2009).
The correlation of 113Cd NMR and 111mCd PAC spectroscopies provides a powerful approach for the characterization of the structure of Cd(II)-substituted Zn(II) proteins.
  Chemistry, 15, 3761-3772.  
16184433 J.Wielens, I.T.Crosby, and D.K.Chalmers (2005).
A three-dimensional model of the human immunodeficiency virus type 1 integration complex.
  J Comput Aided Mol Des, 19, 301-317.
PDB code: 1za9
12609852 M.L.Barreca, K.W.Lee, A.Chimirri, and J.M.Briggs (2003).
Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance.
  Biophys J, 84, 1450-1463.  
11284699 L.S.Busenlehner, N.J.Cosper, R.A.Scott, B.P.Rosen, M.D.Wong, and D.P.Giedroc (2001).
Spectroscopic properties of the metalloregulatory Cd(II) and Pb(II) sites of S. aureus pI258 CadC.
  Biochemistry, 40, 4426-4436.  
10890912 J.C.Chen, J.Krucinski, L.J.Miercke, J.S.Finer-Moore, A.H.Tang, A.D.Leavitt, and R.M.Stroud (2000).
Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding.
  Proc Natl Acad Sci U S A, 97, 8233-8238.
PDB codes: 1ex4 1exq
  10585967 P.Hindmarsh, and J.Leis (1999).
Retroviral DNA integration.
  Microbiol Mol Biol Rev, 63, 836.  
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.