PDBsum entry 1nh9

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protein links
DNA binding protein PDB id
Protein chain
80 a.a. *
Waters ×24
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Crystal structure of a DNA binding protein mja10b from the hyperthermophile methanococcus jannaschii
Structure: DNA-binding protein alba. Chain: a. Synonym: mja10b. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.00Å     R-factor:   0.209     R-free:   0.264
Authors: G.Wang,M.Bartlam,R.Guo,H.Yang,H.Xue,Y.Liu,L.Huang,Z.Rao
Key ref:
G.Wang et al. (2003). Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii. Protein Sci, 12, 2815-2822. PubMed id: 14627741 DOI: 10.1110/ps.03325103
19-Dec-02     Release date:   23-Dec-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q57665  (ALBA_METJA) -  DNA/RNA-binding protein Alba
87 a.a.
80 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biochemical function     nucleic acid binding     4 terms  


DOI no: 10.1110/ps.03325103 Protein Sci 12:2815-2822 (2003)
PubMed id: 14627741  
Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii.
G.Wang, R.Guo, M.Bartlam, H.Yang, H.Xue, Y.Liu, L.Huang, Z.Rao.
The Sac10b family consists of a group of highly conserved DNA binding proteins from both the euryarchaeotal and the crenarchaeotal branches of Archaea. The proteins have been suggested to play an architectural role in the chromosomal organization in these organisms. Previous studies have mainly focused on the Sac10b proteins from the crenarchaeota. Here, we report the 2.0 A resolution crystal structure of Mja10b from the euryarchaeon Methanococcus jannaschii. The model of Mja10b has been refined to an R-factor of 20.9%. The crystal structure of an Mja10b monomer reveals an alpha/beta structure of four beta-strands and two alpha-helices, and Mja10b assembles into a dimer via an extensive hydrophobic interface. Mja10b has a similar topology to that of its crenarchaeota counterpart Sso10b (also known as Alba). Structural comparison between the two proteins suggests that structural features such as hydrophobic inner core, acetylation sites, dimer interface, and DNA binding surface are conserved among Sac10b proteins. Structural differences between the two proteins were found in the loops. To understand the structural basis for the thermostability of Mja10b, the Mja10b structure was compared to other proteins with similar topology. Our data suggest that extensive ion-pair networks, optimized accessible surface area and the dimerization via hydrophobic interactions may contribute to the enhanced thermostability of Mja10b.
  Selected figure(s)  
Figure 3.
Figure 3. (A) The DNA binding surface of the Mja10b dimer. Loop L5 was modeled using the Sso10b structure and is shown as a dashed line. The residues of Lys9 and Lys10 are shown as ball and stick. (B) The electrostatic potential surface of the DNA binding surface of an Mja10b dimer. Positively and negatively charged residues are indicated in blue and red, respectively. Four lysines (Lys9, Lys10, Lys36, and Lys40) are labeled in molecule A. (C) A DNA binding model for the Mja10b dimer. B-form DNA is colored gold and is shown as ball and stick. The Mja10b dimer is shown in blue/cyan. Residues K9 and K10 of each subunit are shown as ball and stick, in red and orange, respectively.
Figure 5.
Figure 5. A stereo figure showing ion-pair interactions in Mja10b. An intrahelix ion-pair is located on helix [2] between E46-R49. The ion-pairs of K59-E28 and R34-D66 connect strands [2] and [3]. The ion-pair network of E62-K60-E82 connects strands [3] and [4].
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 2815-2822) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20082605 C.Jelinska, B.Petrovic-Stojanovska, W.J.Ingledew, and M.F.White (2010).
Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba.
  Biochem J, 427, 49-55.  
19168623 Y.Liu, L.Guo, R.Guo, R.L.Wong, H.Hernandez, J.Hu, Y.Chu, I.J.Amster, W.B.Whitman, and L.Huang (2009).
The Sac10b homolog in Methanococcus maripaludis binds DNA at specific sites.
  J Bacteriol, 191, 2315-2329.  
18323660 K.Hada, T.Nakashima, T.Osawa, H.Shimada, Y.Kakuta, and M.Kimura (2008).
Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Biosci Biotechnol Biochem, 72, 749-758.
PDB code: 2z7c
18004791 T.Kumarevel, K.Sakamoto, S.C.Gopinath, A.Shinkai, P.K.Kumar, and S.Yokoyama (2008).
Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
  Proteins, 71, 1156-1162.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
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