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PDBsum entry 1vk1

Go to PDB code: 
protein ligands metals links
Structural genomics, unknown function PDB id
1vk1
Jmol
Contents
Protein chain
232 a.a. *
Ligands
PO4
PEG
Metals
_NA
Waters ×137
* Residue conservation analysis
PDB id:
1vk1
Name: Structural genomics, unknown function
Title: Conserved hypothetical protein from pyrococcus furiosus pfu-
Structure: Conserved hypothetical protein. Chain: a. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.20Å     R-factor:   0.166     R-free:   0.175
Authors: A.Shah,Z.J.Liu,W.Tempel,L.Chen,D.Lee,H.Yang,J.Chang,M.Zhao,J J.Rose,P.S.Brereton,M.Izumi,F.E.Jenney Jr.,F.L.Poole Ii,C.S F.J.Sugar,M.W.W.Adams,D.C.Richardson,J.S.Richardson,B.C.Wan Southeast Collaboratory For Structural Genomics (Secsg)
Key ref:
N.Shaw et al. (2008). Crystal structure solution of a ParB-like nuclease at atomic resolution. Proteins, 70, 263-267. PubMed id: 17729285 DOI: 10.1002/prot.21641
Date:
13-Apr-04     Release date:   10-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8U3S5  (Q8U3S5_PYRFU) -  Uncharacterized protein
Seq:
Struc:
242 a.a.
232 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  

 

 
DOI no: 10.1002/prot.21641 Proteins 70:263-267 (2008)
PubMed id: 17729285  
 
 
Crystal structure solution of a ParB-like nuclease at atomic resolution.
N.Shaw, W.Tempel, J.Chang, H.Yang, C.Cheng, J.Ng, J.Rose, Z.Rao, B.C.Wang, Z.J.Liu.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall structure of ParB nuclease. (A) A cartoon representation of the ParB nuclease structure. The nuclease is made up of seven helices, eleven -sheets, and numerous loops. The structure could be divided into two domains (colored blue and magenta) according to CATH analysis. (B) A surface electrostatic potential representation of the structure showing the cleft region. The phosphate ligand is buried in a tunnel formed inside the positively charged (blue) cleft. Negative potentials are colored red. The phosphate ligand is shown as sticks and the Ca is represented as a sphere. (C) Putative active site of the ParB-like nuclease with DNA from Eco RV structure (1RVA) superimposed over the cleft region. (D) The primary amino acid sequence of the ParB nuclease annotated with secondary structural elements. Residues making up Domain I are colored blue, while residues forming Domain II are colored magenta. (E) pMD18-T plasmid was treated with purified ParB nuclease (ORI) and the methylated variant (METH) for 60 min at 37°C in a 50 mM Tris-HCl, pH 8.5 buffer, containing 10 mM CaCl[2], 100 mM NaCl, and 1 mM DTT. A control (C) was set up under identical conditions without the protein. The plasmid was degraded by the ParB nuclease.
 
  The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 263-267) copyright 2008.