PDBsum entry 2jsp

Go to PDB code: 
protein links
Gene regulation PDB id
Protein chain
87 a.a. *
* Residue conservation analysis
PDB id:
Name: Gene regulation
Title: The prokaryotic cys2his2 zinc finger adopts a novel fold as revealed by the nmr structure of a. Tumefaciens ros DNA binding domain
Structure: Transcriptional regulatory protein ros. Chain: a. Fragment: DNA binding domain. Engineered: yes
Source: Agrobacterium tumefaciens. Organism_taxid: 358. Gene: ros. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: G.Malgieri
Key ref:
G.Malgieri et al. (2007). The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain. Proc Natl Acad Sci U S A, 104, 17341-17346. PubMed id: 17956987 DOI: 10.1073/pnas.0706659104
10-Jul-07     Release date:   16-Oct-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q04152  (ROS_RHIRD) -  Transcriptional regulatory protein ros
142 a.a.
87 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1073/pnas.0706659104 Proc Natl Acad Sci U S A 104:17341-17346 (2007)
PubMed id: 17956987  
The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
G.Malgieri, L.Russo, S.Esposito, I.Baglivo, L.Zaccaro, E.M.Pedone, B.Di Blasio, C.Isernia, P.V.Pedone, R.Fattorusso.
The first putative prokaryotic Cys(2)His(2) zinc-finger domain has been identified in the transcriptional regulator Ros from Agrobacterium tumefaciens, indicating that the Cys(2)His(2) zinc-finger domain, originally thought to be confined to the eukaryotic kingdom, could be widespread throughout the living kingdom from eukaryotic, both animal and plant, to prokaryotic. In this article we report the NMR solution structure of Ros DNA-binding domain (Ros87), providing 79 structural characterization of a prokaryotic Cys(2)His(2) zinc-finger domain. The NMR structure of Ros87 shows that the putative prokaryotic Cys(2)His(2) zinc-finger sequence is indeed part of a significantly larger zinc-binding globular domain that possesses a novel protein fold very different from the classical fold reported for the eukaryotic classical zinc-finger. The Ros87 globular domain consists of 58 aa (residues 9-66), is arranged in a betabetabetaalphaalpha topology, and is stabilized by an extensive 15-residue hydrophobic core. A backbone dynamics study of Ros87, based on (15)N R(1), (15)N R(2), and heteronuclear (15)N-{(1)H}-NOE measurements, has further confirmed that the globular domain is uniformly rigid and flanked by two flexible tails. Mapping of the amino acids necessary for the DNA binding onto Ros87 structure reveals the protein surface involved in the DNA recognition mechanism of this new zinc-binding protein domain.
  Selected figure(s)  
Figure 5.
Superposition of Ros87 globular domain with the first zinc-finger domain of Tramtrack protein (Protein Data Bank ID code 2DRP), obtained by aligning the four zinc-coordinating residues.
Figure 6.
DNA binding surface of Ros87. (a) Mapping of the residues necessary for DNA binding, as previously determined, onto Ros87 structure, shown as a ribbon drawing. (b and c) Solvent-accessible surface of Ros87 in the same orientation as in a (b) and its rotation of 180° around the z axis (c). Surface properties of Ros87 are blue for positively charged residues and red for negatively charged residues.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20020226 L.Russo, M.Palmieri, I.Baglivo, S.Esposito, C.Isernia, G.Malgieri, P.V.Pedone, and R.Fattorusso (2010).
NMR assignments of the DNA binding domain of Ml4 protein from Mesorhizobium loti.
  Biomol NMR Assign, 4, 55-57.  
19369210 I.Baglivo, L.Russo, S.Esposito, G.Malgieri, M.Renda, A.Salluzzo, B.Di Blasio, C.Isernia, R.Fattorusso, and P.V.Pedone (2009).
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.
  Proc Natl Acad Sci U S A, 106, 6933-6938.  
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.