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PDBsum entry 1vqb
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DNA binding protein PDB id
1vqb

 

 

 

 

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Contents
Protein chain
86 a.a. *
Waters ×45
* Residue conservation analysis
PDB id:
1vqb
Name: DNA binding protein
Title: Gene v protein (single-stranded DNA binding protein)
Structure: Gene v protein. Chain: a. Synonym: gvp, g5p. Engineered: yes
Source: Enterobacteria phage f1. Organism_taxid: 10863. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.198    
Authors: M.M.Skinner,H.Zhang,D.H.Leschnitzer,Y.Guan,H.Bellamy,R.M.Sweet, C.W.Gray,R.N.H.Konings,A.H.-J.Wang,T.C.Terwilliger
Key ref: M.M.Skinner et al. (1994). Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. Proc Natl Acad Sci U S A, 91, 2071-2075. PubMed id: 8134350 DOI: 10.1073/pnas.91.6.2071
Date:
14-Aug-96     Release date:   12-Feb-97    
Supersedes: 1bgh
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P69543  (G5P_BPF1) -  DNA-Binding protein G5P from Enterobacteria phage f1
Seq:
Struc: 		87 a.a.
86 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1073/pnas.91.6.2071 Proc Natl Acad Sci U S A 91:2071-2075 (1994)
PubMed id: 8134350  
 
 
Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.
M.M.Skinner, H.Zhang, D.H.Leschnitzer, Y.Guan, H.Bellamy, R.M.Sweet, C.W.Gray, R.N.Konings, A.H.Wang, T.C.Terwilliger.
 
  ABSTRACT  
 
The crystal structure of the dimeric gene V protein of bacteriophage f1 was determined using multiwavelength anomalous diffraction on the selenomethionine-containing wild-type and isoleucine-47-->methionine mutant proteins with x-ray diffraction data phased to 2.5 A resolution. The structure of the wild-type protein has been refined to an R factor of 19.2% using native data to 1.8 A resolution. The structure of the gene V protein was used to obtain a model for the protein portion of the gene V protein-single-stranded DNA complex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
  19177345 D.E.Tronrud, and B.W.Matthews (2009).
Sorting the chaff from the wheat at the PDB.
  Protein Sci, 18, 2-5.  
19719513 E.Scaltriti, M.Tegoni, C.Rivetti, H.Launay, J.Y.Masson, A.H.Magadan, D.Tremblay, S.Moineau, R.Ramoni, J.Lichière, V.Campanacci, C.Cambillau, and M.Ortiz-Lombardía (2009).
Structure and function of phage p2 ORF34(p2), a new type of single-stranded DNA binding protein.
  Mol Microbiol, 73, 1156-1170.
PDB codes: 2wkc 2wkd
19690089 M.Masso, E.Mathe, N.Parvez, K.Hijazi, and I.I.Vaisman (2009).
Modeling the functional consequences of single residue replacements in bacteriophage f1 gene V protein.
  Protein Eng Des Sel, 22, 665-671.  
18065449 G.Witte, R.Fedorov, and U.Curth (2008).
Biophysical analysis of Thermus aquaticus single-stranded DNA binding protein.
  Biophys J, 94, 2269-2279.  
18453687 T.C.Terwilliger, R.W.Grosse-Kunstleve, P.V.Afonine, N.W.Moriarty, P.D.Adams, R.J.Read, P.H.Zwart, and L.W.Hung (2008).
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.
  Acta Crystallogr D Biol Crystallogr, 64, 515-524.  
15133161 C.Venclovas, K.Ginalski, and C.Kang (2004).
Sequence-structure mapping errors in the PDB: OB-fold domains.
  Protein Sci, 13, 1594-1602.
PDB code: 1s3o
14573944 E.Garman, and J.W.Murray (2003).
Heavy-atom derivatization.
  Acta Crystallogr D Biol Crystallogr, 59, 1903-1913.  
14648774 T.C.Mou, M.C.Shen, T.C.Terwilliger, and D.M.Gray (2003).
Binding and reversible denaturation of double-stranded DNA by Ff gene 5 protein.
  Biopolymers, 70, 637-648.  
12832760 T.C.Terwilliger (2003).
Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement.
  Acta Crystallogr D Biol Crystallogr, 59, 1174-1182.  
14501107 T.C.Terwilliger (2003).
Statistical density modification using local pattern matching.
  Acta Crystallogr D Biol Crystallogr, 59, 1688-1701.  
11809888 T.C.Mou, and D.M.Gray (2002).
The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications.
  Nucleic Acids Res, 30, 749-758.  
11847282 T.C.Mou, N.Sreerama, T.C.Terwilliger, R.W.Woody, and D.M.Gray (2002).
Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions.
  Protein Sci, 11, 601-613.  
12454468 T.C.Terwilliger (2002).
Statistical density modification with non-crystallographic symmetry.
  Acta Crystallogr D Biol Crystallogr, 58, 2082-2086.  
11157767 E.Bochkareva, V.Belegu, S.Korolev, and A.Bochkarev (2001).
Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding.
  EMBO J, 20, 612-618.
PDB code: 1fgu
11478897 J.D.Wen, C.W.Gray, and D.M.Gray (2001).
SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein.
  Biochemistry, 40, 9300-9310.  
11329296 T.C.Mou, C.W.Gray, T.C.Terwilliger, and D.M.Gray (2001).
Ff gene 5 protein has a high binding affinity for single-stranded phosphorothioate DNA.
  Biochemistry, 40, 2267-2275.  
11717488 T.C.Terwilliger (2001).
Map-likelihood phasing.
  Acta Crystallogr D Biol Crystallogr, 57, 1763-1775.  
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
10373006 A.Rojnuckarin, and S.Subramaniam (1999).
Knowledge-based interaction potentials for proteins.
  Proteins, 36, 54-67.  
  9882367 M.Padidam, R.N.Beachy, and C.M.Fauquet (1999).
A phage single-stranded DNA (ssDNA) binding protein complements ssDNA accumulation of a geminivirus and interferes with viral movement.
  J Virol, 73, 1609-1616.  
10049334 T.C.Mou, C.W.Gray, and D.M.Gray (1999).
The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.
  Biophys J, 76, 1537-1551.  
10089316 T.C.Terwilliger, and J.Berendzen (1999).
Automated MAD and MIR structure solution.
  Acta Crystallogr D Biol Crystallogr, 55, 849-861.  
10089362 T.C.Terwilliger, and J.Berendzen (1999).
Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods.
  Acta Crystallogr D Biol Crystallogr, 55, 501-505.  
9585560 T.M.Thompson, B.L.Mark, C.W.Gray, T.C.Terwilliger, N.Sreerama, R.W.Woody, and D.M.Gray (1998).
Circular dichroism and electron microscopy of a core Y61F mutant of the F1 gene 5 single-stranded DNA-binding protein and theoretical analysis of CD spectra of four Tyr --> Phe substitutions.
  Biochemistry, 37, 7463-7477.  
9279126 B.L.Mark, and D.M.Gray (1997).
Tyrosine mutant helps define overlapping CD bands from fd gene 5 protein.nucleic acid complexes.
  Biopolymers, 42, 337-348.  
9164449 D.Suck (1997).
Common fold, common function, common origin?
  Nat Struct Biol, 4, 161-165.  
9230044 R.H.Folmer, M.Nilges, C.H.Papavoine, B.J.Harmsen, R.N.Konings, and C.W.Hilbers (1997).
Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein.
  Biochemistry, 36, 9120-9135.  
  9098886 S.Su, Y.G.Gao, H.Zhang, T.C.Terwilliger, and A.H.Wang (1997).
Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.
  Protein Sci, 6, 771-780.
PDB codes: 1ae2 1ae3 1gkh 1gvp
8612277 A.E.Hodel, P.D.Gershon, X.Shi, and F.A.Quiocho (1996).
The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.
  Cell, 85, 247-256.
PDB code: 1vpt
8706671 B.H.Rietman, P.J.Folkers, R.H.Folmer, G.I.Tesser, and C.W.Hilbers (1996).
The solution structure of the synthetic circular peptide CGVSRQGKPYC. NMR studies of the folding of a synthetic model for the DNA-binding loop of the ssDNA-binding protein encoded by gene V of phage M13.
  Eur J Biochem, 238, 706-713.  
8909284 C.R.Robinson, and R.T.Sauer (1996).
Equilibrium stability and sub-millisecond refolding of a designed single-chain Arc repressor.
  Biochemistry, 35, 13878-13884.  
8653795 H.S.Subramanya, A.J.Doherty, S.R.Ashford, and D.B.Wigley (1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
  Cell, 85, 607-615.
PDB code: 1a0i
8855252 M.M.Skinner, and T.C.Terwilliger (1996).
Potential use of additivity of mutational effects in simplifying protein engineering.
  Proc Natl Acad Sci U S A, 93, 10753-10757.
PDB codes: 1vqa 1vqc 1vqd 1vqe 1vqg 1vqh
8634294 P.C.Swanson, C.Ackroyd, and G.D.Glick (1996).
Ligand recognition by anti-DNA autoantibodies. Affinity, specificity, and mode of binding.
  Biochemistry, 35, 1624-1633.  
8988001 T.C.Terwilliger (1996).
Gene V protein dimerization and cooperativity of binding of poly(dA).
  Biochemistry, 35, 16652-16664.  
8608120 T.N.Jaishree, V.Ramakrishnan, and S.W.White (1996).
Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.
  Biochemistry, 35, 2845-2853.  
8692937 X.Cheng, A.C.Harms, P.N.Goudreau, T.C.Terwilliger, and R.D.Smith (1996).
Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry.
  Proc Natl Acad Sci U S A, 93, 7022-7027.  
7601089 A.R.Bernard, T.N.Wells, A.Cleasby, F.Borlat, M.A.Payton, and A.E.Proudfoot (1995).
Selenomethionine labelling of phosphomannose isomerase changes its kinetic properties.
  Eur J Biochem, 230, 111-118.  
7556200 J.J.Prompers, R.H.Folmer, M.Nilges, P.J.Folkers, R.N.Konings, and C.W.Hilbers (1995).
Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.
  Eur J Biochem, 232, 506-514.
PDB codes: 2gva 2gvb
  7556054 R.H.Folmer, M.Nilges, R.N.Konings, and C.W.Hilbers (1995).
Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.
  EMBO J, 14, 4132-4142.
PDB code: 1pfs
  7757008 Y.Guan, H.Zhang, and A.H.Wang (1995).
Electrostatic potential distribution of the gene V protein from Ff phage facilitates cooperative DNA binding: a model of the GVP-ssDNA complex.
  Protein Sci, 4, 187-197.
PDB code: 1gpv
7565651 A.P.Stassen, R.H.Folmer, C.W.Hilbers, and R.N.Konings (1994).
Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics.
  Mol Biol Rep, 20, 109-127.  
7925383 R.H.Folmer, P.J.Folkers, A.Kaan, A.J.Jonker, J.M.Aelen, R.N.Konings, and C.W.Hilbers (1994).
Secondary structure of the single-stranded DNA binding protein encoded by filamentous phage Pf3 as determined by NMR.
  Eur J Biochem, 224, 663-676.  
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.

 

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