PDBsum entry 2hax

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protein dna_rna ligands metals Protein-protein interface(s) links
Gene regulation/DNA PDB id
Protein chains
66 a.a. *
MPD ×2
Waters ×234
* Residue conservation analysis
PDB id:
Name: Gene regulation/DNA
Title: Crystal structure of bacillus caldolyticus cold shock protein in complex with hexathymidine
Structure: 5'-d( Tp Tp Tp Tp Tp T)-3'. Chain: c, d. Synonym: hexathymidine. Engineered: yes. Cold shock protein cspb. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: synthetic deoxyribonucleotide. Bacillus caldolyticus. Organism_taxid: 1394. Gene: cspb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.29Å     R-factor:   0.132     R-free:   0.162
Authors: K.E.A.Max,U.Heinemann
Key ref:
K.E.Max et al. (2007). Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus. FEBS J, 274, 1265-1279. PubMed id: 17266726 DOI: 10.1111/j.1742-4658.2007.05672.x
13-Jun-06     Release date:   24-Apr-07    
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Protein chains
Pfam   ArchSchema ?
P41016  (CSPB_BACCL) -  Cold shock protein CspB
66 a.a.
66 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     nucleic acid binding     2 terms  


DOI no: 10.1111/j.1742-4658.2007.05672.x FEBS J 274:1265-1279 (2007)
PubMed id: 17266726  
Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.
K.E.Max, M.Zeeb, R.Bienert, J.Balbach, U.Heinemann.
Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP (Bc-Csp) in complex with hexathymidine (dT(6)) at a resolution of 1.29 A. Bound to dT(6), crystalline Bc-Csp forms a domain-swapped dimer in which beta strands 1-3 associate with strands 4 and 5 from the other subunit to form a closed beta barrel and vice versa. The globular units of dimeric Bc-Csp closely resemble the well-known structure of monomeric CSP. Structural reorganization from the monomer to the domain-swapped dimer involves a strictly localized change in the peptide bond linking Glu36 and Gly37 of Bc-Csp. Similar structural reorganizations have not been found in any other CSP or oligonucleotide/oligosaccharide-binding fold structures. Each dT(6) ligand is bound to one globular unit of Bc-Csp via an amphipathic protein surface. Individual binding subsites interact with the DNA bases through stacking and hydrogen bonding. The sugar-phosphate backbone remains solvent exposed. Based on crystallographic and biochemical studies of deoxyoligonucleotide binding to CSP, we suggest a common mode of binding of single-stranded heptanucleotide motifs to proteins containing cold shock domains, including the eukaryotic Y-box factors.
  Selected figure(s)  
Figure 1.
Fig. 1. Crystal structure of The Bc-Csp·dT[6] complex. (A) The DNA strands (red = backbone, beige = bases) bind to globular units of a swapped Bc-Csp dimer (green = chain A, blue = chain B). Each globular unit is composed of residues 1–35 and 38–66 of two different protein chains. The base of the terminal nucleotide T6 occupies two different positions in chain D (dotted arrow). (B) The region of the domain swap in chain B revealed by F[o] – F[c] difference electron density calculated from a model devoid of residues 35–38. The map (grey wire frame) was contoured at 2.5 .
Figure 9.
Fig. 9. The ligand-binding surfaces of CSP and Y-box proteins are highly conserved. (A) CSP sequence conservation mapped to the surface of Bc-Csp bound to dT[6]. Most residues forming the ligand interaction site are conserved on the level of at least 75% identity (dark green) and similarity (light green). Invariant regions which originate from the protein backbone are coloured light blue. The monomeric structure shown in this figure represents a globular unit from a swapped Bc-Csp dimer. The model of heptanucleotide ligand (sticks) was assembled by combining structural information of the Bs-CspB·dT[6] and Bc-Csp·dT[6] complex structures. (B) Sequence alignment of CSP (upper) and Y-box proteins (lower). Residues which are conserved at a level of at least 75% identity or similarity are highlighted in black or grey, respectively. Side chains involved in DNA binding in the Bc-Csp crystal structure are marked by triangles (blue = polar contacts, yellow = hydrophobic contacts, green = both).
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2007, 274, 1265-1279) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21426380 N.Mojib, D.T.Andersen, and A.K.Bej (2011).
Structure and function of  a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica.
  FEMS Microbiol Lett, 319, 106-114.  
20607520 H.Balhesteros, R.R.Mazzon, C.A.da Silva, E.A.Lang, and M.V.Marques (2010).
CspC and CspD are essential for Caulobacter crescentus stationary phase survival.
  Arch Microbiol, 192, 747-758.  
20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
  Annu Rev Biochem, 79, 233-269.  
19145605 A.L.Stewart, and M.L.Waters (2009).
Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.
  Chembiochem, 10, 539-544.  
19459942 G.Batta, T.Barna, Z.Gáspári, S.Sándor, K.E.Kövér, U.Binder, B.Sarg, L.Kaiserer, A.K.Chhillar, A.Eigentler, E.Leiter, N.Hegedüs, I.Pócsi, H.Lindner, and F.Marx (2009).
Functional aspects of the solution structure and dynamics of PAF--a highly-stable antifungal protein from Penicillium chrysogenum.
  FEBS J, 276, 2875-2890.
PDB code: 2kcn
19564956 K.M.Guardino, S.R.Sheftic, R.E.Slattery, and A.T.Alexandrescu (2009).
Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily.
  Int J Mol Sci, 10, 2412-2430.  
  18391418 J.Ren, J.E.Nettleship, S.Sainsbury, N.J.Saunders, and R.J.Owens (2008).
Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 247-251.
PDB code: 3cam
17661445 E.Watson, W.M.Matousek, E.L.Irimies, and A.T.Alexandrescu (2007).
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins.
  Biochemistry, 46, 9484-9494.  
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