PDBsum entry: 2gbz

Hydrolase

PDB id: 2gbz

Contents

Protein chain

179 a.a. *

Metals

_MG

Waters ×70

* Residue conservation analysis

PDB id:

2gbz

Name:

Hydrolase

Title:

The crystal structure of xc847 from xanthomonas campestris: oligoribonuclease of dnaq fold family with a novel opposing helix

Structure:

Oligoribonuclease. Chain: a. Engineered: yes

Source:

Xanthomonas campestris pv. Campestris. Organism_taxid: 340. Strain: pv. Campestris. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.203 R-free: 0.263

Authors:

K.H.Chin,C.Y.Yang,C.C.Chou,A.H.J.Wang,S.H.Chou

Key ref:

K.H.Chin et al. (2006). The crystal structure of XC847 from Xanthomonas campestris: a 3'-5' oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix. Proteins, 65, 1036-1040. PubMed id: 17029243 DOI: 10.1002/prot.21148

Date:

12-Mar-06 Release date: 16-Jan-07

Protein chain

Q8P8S1  (ORN_XANCP) -  Oligoribonuclease

Seq: 194 a.a.

Struc: 179 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (2 terms)
• Biochemical function: nucleic acid binding (5 terms)

DOI no: 10.1002/prot.21148

Proteins 65:1036-1040 (2006)

PubMed id: 17029243

The crystal structure of XC847 from Xanthomonas campestris: a 3'-5' oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix.

K.H.Chin, C.Y.Yang, C.C.Chou, A.H.Wang, S.H.Chou.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Structure of Xanthomonas campestris XC847 (all figures were produced with PdbViewer[15] except Figure 2(b) that was produced with Pymol (DeLano Scientific, USA). (a) Diagram showing the secondary structure elements in XC847 superimposed on its primary sequence with helices (in green tubes) labeled consecutively from A- I, -strands (in red arrows) from 1- 5. The four highly conserved motifs I, II, III, and IV are boxed in green. The four active site acidic residues Asp15, Glu17, Asp115, and Asp166 are shown in red, and the highly conserved residues in motifs I, II, III, and IV in blue. (b) The ribbon diagram of XC847 structure color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. Helices A- I and -strands 1- 5 are indicated. The four active site acidic residues are shown in ball-and-stick and their positions in the crevice marked by a pink arrow. (c) Active site structure of XC847. Coordinate bonds between Mg^2+ ion and ligands were shown as green dotted lines.

Figure 2.
Figure 2. (a) The ribbon diagram of the crystal structure of XC847 dimer. The pink dotted line indicates the noncrystallographic 2-fold symmetry. The Asp24 and His120 residues participating in inter-subunit H-bonds and Cys113 residues in inter-subunit disulfide bond are shown in ball-and-stick. (b) The electrostatic surface plot of XC847 dimer drawn in the same orientation as (a). The positive surface was drawn in blue and negative surface in red. The active site was marked by a red dotted arrow and the substrate binding site a cyan dotted arrow. (c) Superimposed pictures of XC847 structure (red) with 1WLJ (blue),[6] 1J54 (yellow),[7] and 1FXX (green) structures.[8] The hinge position for the different orientation of H helices are marked with a dotted blue arrow. The invisible loop residues of 1WLJ and 1FXX are connected by dotted lines. (d) The modeling study of the U5 oligonucleotide binding to XC847 dimer shown in stereo. The U5 substrate (shown in red) fits well into the crevice between the XC847 dimer (one was shown in blue and another in green), and experiences no steric hindrance. The coordination bonds between the active site residues Asp15, Glu17, Asp166, and the substrate U[5]O1p atom with the Mg^2+ were drawn in dotted red lines, while the salt bridges and H-bonds between the XC847 dimer and the U5 substrate in green dotted lines.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 1036-1040) copyright 2006.