PDBsum entry: 2apj

Structural genomics, unknown function

PDB id: 2apj

Contents

Protein chains

244 a.a. *

Waters ×1611

* Residue conservation analysis

PDB id:

2apj

Name:

Structural genomics, unknown function

Title:

X-ray structure of protein from arabidopsis thaliana at4g342 angstrom resolution

Structure:

Putative esterase. Chain: a, b, c, d. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at4g34215. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.147 R-free: 0.183

Authors:

G.E.Wesenberg,G.N.Phillips Jr.,J.G.Mccoy,E.Bitto,C.A.Bingman S.T.Allard,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

E.Bitto et al. (2005). The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana. Acta Crystallogr D Biol Crystallogr, 61, 1655-1661. PubMed id: 16301800 DOI: 10.1107/S0907444905034074

Date:

16-Aug-05 Release date: 30-Aug-05

Supersedes:

2aea

Protein chains

Q8L9J9  (CAES_ARATH) -  Probable carbohydrate esterase At4g34215

Seq: 260 a.a.

Struc: 244 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cellular_component (1 term)
• Biological process: biological_process (1 term)
• Biochemical function: hydrolase activity (1 term)

DOI no: 10.1107/S0907444905034074

Acta Crystallogr D Biol Crystallogr 61:1655-1661 (2005)

PubMed id: 16301800

The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana.

E.Bitto, C.A.Bingman, J.G.McCoy, S.T.Allard, G.E.Wesenberg, G.N.Phillips.

ABSTRACT

The crystal structure of the At4g34215 protein of Arabidopsis thaliana was determined by molecular replacement and refined to an R factor of 14.6% (R(free) = 18.3%) at 1.6 Angstroms resolution. The crystal structure confirms that At4g34215 belongs to the SGNH-hydrolase superfamily of enzymes. The catalytic triad of the enzyme comprises residues Ser31, His238 and Asp235. In this structure the catalytic serine residue was found to be covalently modified, possibly by phenylmethylsulfonyl fluoride. The structure also reveals a previously undescribed variation within the active site. The conserved asparagine from block III, which provides a hydrogen bond for an oxyanion hole in the SGNH-hydrolase superfamily enzymes, is missing in At4g34215 and is functionally replaced by Gln30 from block I. This residue is positioned in a catalytically competent conformation by nearby residues, including Gln159, Gly160 and Glu161, which are fully conserved in the carbohydrate esterase family 6 enzymes.

Selected figure(s)

Figure 1.
Figure 1 (a) A topology diagram of the At4g34215 structure (PDB code [115]1apj ). The central seven-stranded [116][beta] -sheet (red arrows) is surrounded by several helices (cyan cylinders) and the auxiliary two-stranded [117][beta] -sheet comprising [118][beta] -strands ab (cyan arrows). (b) A ribbon diagram of the At4g34215 structure with rainbow coloring from amino-terminus (blue) to carboxy-terminus (red). The catalytic triad residues Ser31, His238 and Asp235 are depicted in stick representation. The structure is labeled to match the topology diagram.

Figure 2.
Figure 2 Structural superposition of A. thaliana At4g34215 (red; PDB code [146]2apj ) and CAC0529 (cyan; PDB code [147]1zmb ). The catalytic triad residues Ser31, His238 and Asp235 of At4g34215 are depicted in stick representation (blue). The carboxy-terminus of CAC0529 and surface loops showing the most notable differences are labeled for convenience.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1655-1661) copyright 2005.

Figures were selected by an automated process.