PDBsum entry 1vel

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protein ligands metals Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
(+ 0 more) 163 a.a. *
SO4 ×2
_CD ×10
_NA ×2
Waters ×217
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Mycobacterium smegmatis dps tetragonal form
Structure: Starvation-induced DNA protecting protein. Chain: a, b, c, d, e, f. Synonym: dps. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dodecamer (from PDB file)
2.99Å     R-factor:   0.183     R-free:   0.210
Authors: S.Roy,S.Gupta,S.Das,K.Sekar,D.Chatterji,M.Vijayan
Key ref:
S.Roy et al. (2004). X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules. J Mol Biol, 339, 1103-1113. PubMed id: 15178251 DOI: 10.1016/j.jmb.2004.04.042
01-Apr-04     Release date:   29-Jun-04    
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Protein chains
Pfam   ArchSchema ?
P0C558  (DPS_MYCSM) -  DNA protection during starvation protein
183 a.a.
163 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     response to stress   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  


DOI no: 10.1016/j.jmb.2004.04.042 J Mol Biol 339:1103-1113 (2004)
PubMed id: 15178251  
X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules.
S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan.
The structure of the DNA binding protein from starved cells from Mycobacterium smegmatis has been determined in three crystal forms and has been compared with those of similar proteins from other sources. The dodecameric molecule can be described as a distorted icosahedron. The interfaces among subunits are such that the dodecameric molecule appears to have been made up of stable trimers. The situation is similar in the proteins from Escherichia coli and Agrobacterium tumefaciens, which are closer to the M.smegmatis protein in sequence and structure than those from other sources, which appear to form a dimer first. Trimerisation is aided in the three proteins by the additional N-terminal stretches that they possess. The M.smegmatis protein has an additional C-terminal stretch compared to other related proteins. The stretch, known to be involved in DNA binding, is situated on the surface of the molecule. A comparison of the available structures permits a delineation of the rigid and flexible regions in the molecule. The subunit interfaces around the molecular dyads, where the ferroxidation centres are located, are relatively rigid. Regions in the vicinity of the acidic holes centred around molecular 3-fold axes, are relatively flexible. So are the DNA binding regions. The crystal structures of the protein from M.smegmatis confirm that DNA molecules can occupy spaces within the crystal without disturbing the arrangement of the protein molecules. However, contrary to earlier suggestions, the spaces do not need to be between layers of protein molecules. The cubic form provides an arrangement in which grooves, which could hold DNA molecules, criss-cross the crystal.
  Selected figure(s)  
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2004, 339, 1103-1113) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21283627 P.Ghatak, K.Karmakar, S.Kasetty, and D.Chatterji (2011).
Unveiling the role of dps in the organization of mycobacterial nucleoid.
  PLoS One, 6, e16019.  
19956571 R.Saraswathi, R.Pait Chowdhury, S.M.Williams, P.Ghatak, and D.Chatterji (2009).
The mycobacterial MsDps2 protein is a nucleoid-forming DNA binding protein regulated by sigma factors sigma and sigma.
  PLoS One, 4, e8017.  
18453691 P.S.Kaushal, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
  Acta Crystallogr D Biol Crystallogr, 64, 551-560.
PDB code: 2zhx
16345079 A.Thumiger, A.Polenghi, E.Papinutto, R.Battistutta, C.Montecucco, and G.Zanotti (2006).
Crystal structure of antigen TpF1 from Treponema pallidum.
  Proteins, 62, 827-830.
PDB code: 2fjc
16855817 C.V.Romão, E.P.Mitchell, and S.McSweeney (2006).
The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.
  J Biol Inorg Chem, 11, 891-902.
PDB codes: 2c2f 2c2u
  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
  16946478 M.Selvaraj, N.S.Singh, S.Roy, R.Sangeetha, U.Varshney, and M.Vijayan (2006).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 913-915.  
  17142904 P.Singh, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2006).
Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1231-1234.  
16699190 S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2006).
Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK.
  Acta Crystallogr D Biol Crystallogr, 62, 628-638.
PDB codes: 2ges 2get 2geu 2gev
17018059 S.Franceschini, P.Ceci, F.Alaleona, E.Chiancone, and A.Ilari (2006).
Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus.
  FEBS J, 273, 4913-4928.
PDB code: 2c41
16861227 X.Liu, K.Kim, T.Leighton, and E.C.Theil (2006).
Paired Bacillus anthracis Dps (mini-ferritin) have different reactivities with peroxide.
  J Biol Chem, 281, 27827-27835.  
16091046 A.T.Pulliainen, A.Kauko, S.Haataja, A.C.Papageorgiou, and J.Finne (2005).
Dps/Dpr ferritin-like protein: insights into the mechanism of iron incorporation and evidence for a central role in cellular iron homeostasis in Streptococcus suis.
  Mol Microbiol, 57, 1086-1100.  
16024730 B.Wiedenheft, J.Mosolf, D.Willits, M.Yeager, K.A.Dryden, M.Young, and T.Douglas (2005).
An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 102, 10551-10556.  
16041080 K.Saikrishnan, G.P.Manjunath, P.Singh, J.Jeyakanthan, Z.Dauter, K.Sekar, K.Muniyappa, and M.Vijayan (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.
PDB codes: 1x3e 1x3f 1x3g
16030020 P.Ceci, A.Ilari, E.Falvo, L.Giangiacomo, and E.Chiancone (2005).
Reassessment of protein stability, DNA binding, and protection of Mycobacterium smegmatis Dps.
  J Biol Chem, 280, 34776-34785.
PDB code: 1uvh
  16508093 S.Das, P.Kumar, V.Bhor, A.Surolia, and M.Vijayan (2005).
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 65-67.  
16091047 T.J.Stillman, M.Upadhyay, V.A.Norte, S.E.Sedelnikova, M.Carradus, S.Tzokov, P.A.Bullough, C.A.Shearman, M.J.Gasson, C.H.Williams, P.J.Artymiuk, and J.Green (2005).
The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N-terminal helix that is required for DNA binding.
  Mol Microbiol, 57, 1101-1112.
PDB codes: 1zs3 1zuj
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.