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DNA binding protein/DNA PDB id
1azq
Jmol
Contents
Protein chain
66 a.a.
DNA/RNA
Waters ×68
PDB id:
1azq
Name: DNA binding protein/DNA
Title: Hyperthermophile chromosomal protein sac7d bound with kinked DNA duplex
Structure: DNA (5'-d( Gp Tp Ap Ap Tp Tp Ap C)-3'). Chain: b, c. Engineered: yes. Protein (hyperthermophile chromosomal protein sac7d). Chain: a. Synonym: 7 kd hyperthermophile DNA-binding protein. Engineered: yes
Source: Synthetic: yes. Sulfolobus acidocaldarius. Organism_taxid: 2285. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
1.94Å     R-factor:   0.186     R-free:   0.238
Authors: H.Robinson,Y.-G.Gao,B.S.Mccrary,S.P.Edmondson,J.W.Shriver, A.H.-J.Wang
Key ref:
H.Robinson et al. (1998). The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 202-205. PubMed id: 9515968 DOI: 10.1038/32455
Date:
20-Nov-97     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13123  (DN71_SULAC) -  DNA-binding protein 7d
Seq:
Struc: 		66 a.a.
66 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1038/32455 Nature 392:202-205 (1998)
PubMed id: 9515968  
 
 
The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.
H.Robinson, Y.G.Gao, B.S.McCrary, S.P.Edmondson, J.W.Shriver, A.H.Wang.
 
  ABSTRACT  
 
The proteins Sac7d and Sso7d belong to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius and S. solfactaricus, respectively. These proteins are extremely stable to heat, acid and chemical agents. Sac7d binds to DNA without any particular sequence preference and thereby increases its melting temperature by approximately 40 degrees C. We have now solved and refined the crystal structure of Sac7d in complex with two DNA sequences to high resolution. The structures are examples of a nonspecific DNA-binding protein bound to DNA, and reveal that Sac7d binds in the minor groove, causing a sharp kinking of the DNA helix that is more marked than that induced by any sequence-specific DNA-binding proteins. The kink results from the intercalation of specific hydrophobic side chains of Sac7d into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Sequence of Sac7d and Sso7d, and structure of Sac7d-DNA complexes. a, Amino-acid sequences of recombinant Sac7d and Sso7d. The first methionine is from the initiation codon. b, The (2F[o] - F[c]) Fourier electron density maps (contoured at 1 level) of the regions at the interface of protein and DNA. c, Ribbon diagrams of the structure of two Sac7d-DNA complexes drawn by MIDAS.27 		Figure 3.
Figure 3 Sac7d-DNA contacts. Left, schematic diagram summarizing all Sac7d-DNA contacts. The filled, open and dashed arrows represent direct hydrogen bonds or salt bridges, respectively. Right, the protein-DNA contacts of the Sac7d-GCGATCGC complex using the triple-stranded -sheet of Sac7d. Selected side chains of Sac7d are shown.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 392, 202-205) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Thermophilic and halophilic extremophiles.
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10215851 Y.G.Gao, H.Robinson, and A.H.Wang (1999).
High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).
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PDB codes: 440d 441d
9665172 P.Agback, H.Baumann, S.Knapp, R.Ladenstein, and T.Härd (1998).
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PDB code: 1bbx
9580681 P.López-García, S.Knapp, R.Ladenstein, and P.Forterre (1998).
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The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
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PDB codes: 1bf4 1bnz
9782777 D.Suck (1997).
DNA recognition by structure-selective nucleases.
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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.