PDBsum entry 2f8h

Hydrolase

PDB id

2f8h

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Contents

			Protein chain

					360 a.a. *

			Waters ×351

* Residue conservation analysis

PDB id:

2f8h

Links

Name:

Hydrolase

Title:

Structure of acetylcitrulline deacetylase from xanthomonas campestris in metal-free form

Structure:

Aectylcitrulline deacetylase. Chain: a. Synonym: acetylornithine deacetylase. Engineered: yes

Source:

Xanthomonas campestris. Organism_taxid: 339. Strain: atcc 33913. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.75Å

R-factor:

0.226

R-free:

0.258

Authors:

D.Shi,X.Yu,L.Roth,N.M.Allewell,M.Tuchman

Key ref:

D.Shi et al. (2007). Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris. Biophys Chem, 126, 86-93. PubMed id: 16750290

Date:

02-Dec-05

Release date:

26-Sep-06

PROCHECK

	Headers

	References

Protein chain

A0A0H2X6W0 (A0A0H2X6W0_XANC8) - N-acetyl-L-citrulline deacetylase from Xanthomonas campestris pv. campestris (strain 8004)

Seq: Struc:					366 a.a. 360 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.5.1.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Biophys Chem 126:86-93 (2007)
PubMed id: 16750290

Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris.
D.Shi, X.Yu, L.Roth, M.Tuchman, N.M.Allewell.

ABSTRACT

The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 A resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in conformation. The dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two beta strands that form a continuous beta sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl of the acetyl group.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20138056

B.P.Nocek, D.M.Gillner, Y.Fan, R.C.Holz, and A.Joachimiak (2010).
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.

J Mol Biol, 397, 617-626.

PDB codes:

3ic1 3isz

17600144

D.Shi, X.Yu, J.Cabrera-Luque, T.Y.Chen, L.Roth, H.Morizono, N.M.Allewell, and M.Tuchman (2007).
A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase.

Protein Sci, 16, 1689-1699.

PDB codes:

2g65 2g68 2g6a 2g6c 2g7m 3l02 3l04 3l05 3l06

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 codes are shown on the right.