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PDBsum entry 2fvq

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protein dna_rna links
Transferase/DNA PDB id
2fvq
Jmol
Contents
Protein chain
255 a.a. *
DNA/RNA
Waters ×130
* Residue conservation analysis
PDB id:
2fvq
Name: Transferase/DNA
Title: A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus
Structure: 5'- d( Cp Tp Tp Tp Cp Ap Tp Tp Ap Ap Tp Gp Ap Ap Ap G)-3'. Chain: b. Engineered: yes. Reverse transcriptase. Chain: a. Synonym: rt. Engineered: yes
Source: Synthetic: yes. Moloney murine leukemia virus. Organism_taxid: 11801. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.236     R-free:   0.263
Authors: S.P.Montano,M.L.Cote,M.J.Roth,M.M.Georgiadis
Key ref: S.P.Montaño et al. (2006). Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus. Nucleic Acids Res, 34, 5353-5360. PubMed id: 17003051
Date:
31-Jan-06     Release date:   12-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03355  (POL_MLVMS) -  Gag-Pol polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1738 a.a.
255 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.7.7.49  - 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 3: E.C.2.7.7.7  - 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 4: E.C.3.1.26.4  - Ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
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!
  Biological process     RNA-dependent DNA replication   1 term 
  Biochemical function     RNA binding     2 terms  

 

 
    reference    
 
 
Nucleic Acids Res 34:5353-5360 (2006)
PubMed id: 17003051  
 
 
Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus.
S.P.Montaño, M.L.Coté, M.J.Roth, M.M.Georgiadis.
 
  ABSTRACT  
 
In the first step of retroviral integration, integrase cleaves the linear viral DNA within its long terminal repeat (LTR) immediately 3' to the CA dinucleotide step, resulting in a reactive 3' OH on one strand and a 5' two base overhang on the complementary strand. In order to investigate the structural properties of the 3' end processing site within the Moloney murine leukemia virus (MMLV) LTR d(TCTTTCATT), a host-guest crystallographic method was employed to determine the structures of four self-complementary 16 bp oligonucleotides including LTR sequences (underlined), d(TTTCATTGCAATGAAA), d(CTTTCATTAATGAAAG), d(TCTTTCATATGAAAGA) and d(CACAATGATCATTGTG), the guests, complexed with the N-terminal fragment of MMLV reverse transcriptase, the host. The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice. Properties unique to the CA dinucleotide step within the LTR sequence, independent of its position from the end of the duplex, include a positive roll angle and negative slide value. This propensity for the CA dinucleotide step within the MMLV LTR sequence to adopt only positive roll angles is likely influenced by the more rigid, invariable 3' and 5' flanking TT dinucleotide steps and may be important for specific recognition and/or cleavage by the MMLV integrase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19405506 L.S.Glass, B.Nguyen, K.D.Goodwin, C.Dardonville, W.D.Wilson, E.C.Long, and M.M.Georgiadis (2009).
Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA.
  Biochemistry, 48, 5943-5952.
PDB code: 3fsi
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.