spacer
spacer

PDBsum entry 1x3e
Go to PDB code: 
protein metals Protein-protein interface(s) links
DNA binding protein PDB id
1x3e

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
110 a.a. *
119 a.a. *
Metals
_CD
Waters ×243
* Residue conservation analysis
PDB id:
1x3e
Name: DNA binding protein
Title: Crystal structure of the single-stranded DNA-binding protein from mycobacterium smegmatis
Structure: Single-strand binding protein. Chain: a, b. Synonym: single-stranded DNA-binding protein, ssb, helix- destabilizing protein. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.15Å     R-factor:   0.202     R-free:   0.239
Authors: K.Saikrishnan,G.P.Manjunath,P.Singh,J.Jeyakanthan,Z.Dauter,K.Sekar, K.Muniyappa,M.Vijayan
Key ref:
K.Saikrishnan et al. (2005). Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association. Acta Crystallogr D Biol Crystallogr, 61, 1140-1148. PubMed id: 16041080 DOI: 10.1107/S0907444905016896
Date:
04-May-05     Release date:   15-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9AFI5  (SSB_MYCS2) -  Single-stranded DNA-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
Seq:
Struc: 		165 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
Q9AFI5  (SSB_MYCS2) -  Single-stranded DNA-binding protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
Seq:
Struc: 		165 a.a.
119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1107/S0907444905016896 Acta Crystallogr D Biol Crystallogr 61:1140-1148 (2005)
PubMed id: 16041080  
 
 
Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association.
K.Saikrishnan, G.P.Manjunath, P.Singh, J.Jeyakanthan, Z.Dauter, K.Sekar, K.Muniyappa, M.Vijayan.
 
  ABSTRACT  
 
The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its homologue from Mycobacterium tuberculosis, indicating that the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer are characteristic features of mycobacterial SSBs. The central OB fold is conserved in mycobacterial SSBs as well as those from Escherichia coli, Deinococcus radiodurans and human mitochondria. However, the quaternary structure exhibits considerable variability. The observed plasticity of the subunit is related to this variability. The crystal structures and modelling provide a rationale for the variability. The strand involved in the clamp mechanism, which leads to higher stability of the tetramer, appears to occur in all high-G+C Gram-positive bacteria. The higher stability is perhaps required by these organisms. The mode of DNA binding of mycobacterial SSBs is different from that of E. coli SSB partly on account of the difference in the shape of the tetramers. Another difference between the two modes is that the former contains additional ionic interactions and is more susceptible to salt concentration.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 A 2F[o] - F[c] omit map for the stretch of residues 102-120. The figure was generated using BOBSCRIPT (Esnouf, 1997 [Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.]-[bluearr.gif] ). The map was contoured at 1 [sigma] . 		Figure 6.
Figure 6 Surface diagram of MsSSB, DrSSB and EcSSB viewed down the twofold axis P (represented as a blue ball), highlighting the variation in the orientation of the OB folds. Subunits A and C of MsSSB and EcSSB and subunit A of DrSSB were superposed onto one another (represented in grey) to bring out the difference in the orientation of subunits B and D of MsSSB (magenta) and EcSSB (red) and subunit B of DrSSB (green). The loops are omitted for clarity.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1140-1148) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21132356 H.C.Jan, Y.L.Lee, and C.Y.Huang (2011).
Characterization of a Single-Stranded DNA-Binding Protein from Pseudomonas aeruginosa PAO1.
  Protein J, 30, 20-26.  
20969962 M.Wu, Y.J.Park, E.Pardon, S.Turley, A.Hayhurst, J.Deng, J.Steyaert, and W.G.Hol (2011).
Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies.
  J Struct Biol, 174, 124-136.
PDB codes: 3k7u 3k80 3k81
21267641 Y.H.Huang, Y.L.Lee, and C.Y.Huang (2011).
Characterization of a Single-Stranded DNA Binding Protein from Salmonella enterica Serovar Typhimurium LT2.
  Protein J, 30, 102-108.  
20795631 A.G.Kozlov, J.M.Eggington, M.M.Cox, and T.M.Lohman (2010).
Binding of the dimeric Deinococcus radiodurans single-stranded DNA binding protein to single-stranded DNA.
  Biochemistry, 49, 8266-8275.  
20944238 P.S.Kaushal, P.Singh, A.Sharma, K.Muniyappa, and M.Vijayan (2010).
X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures.
  Acta Crystallogr D Biol Crystallogr, 66, 1048-1058.
PDB codes: 3afp 3afq
19400798 B.Marintcheva, U.Qimron, Y.Yu, S.Tabor, and C.Richardson (2009).
Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C-terminal phenylalanine.
  Mol Microbiol, 72, 869-880.  
19571366 L.Shokri, I.Rouzina, and M.C.Williams (2009).
Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA.
  Phys Biol, 6, 25002.  
18238893 B.Marintcheva, A.Marintchev, G.Wagner, and C.C.Richardson (2008).
Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface.
  Proc Natl Acad Sci U S A, 105, 1855-1860.  
17348019 D.Das, H.Hyun, Y.Lou, H.Yokota, R.Kim, and S.H.Kim (2007).
Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae.
  Proteins, 67, 776-782.
PDB code: 2hql
  16880543 J.R.Prabu, S.Thamotharan, J.S.Khanduja, E.Z.Alipio, C.Y.Kim, G.S.Waldo, T.C.Terwilliger, B.Segelke, T.Lekin, D.Toppani, L.W.Hung, M.Yu, E.Bursey, K.Muniyappa, N.R.Chandra, and M.Vijayan (2006).
Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 731-734.
PDB code: 2h5x
17148487 R.Fedorov, G.Witte, C.Urbanke, D.J.Manstein, and U.Curth (2006).
3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins.
  Nucleic Acids Res, 34, 6708-6717.
PDB codes: 2ihe 2ihf
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.

 

spacer
spacer