PDBsum entry: 1l6r

Structural genomics, unknown function

PDB id: 1l6r

Contents

Protein chains

225 a.a. *

Ligands

FMT

Metals

_CA ×5

Waters ×715

* Residue conservation analysis

PDB id:

1l6r

Name:

Structural genomics, unknown function

Title:

Crystal structure of thermoplasma acidophilum 0175 (apc0014)

Structure:

Hypothetical protein ta0175. Chain: a, b. Engineered: yes

Source:

Thermoplasma acidophilum. Organism_taxid: 2303. Gene: ta0175. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.40Å R-factor: 0.171 R-free: 0.195

Authors:

Y.Kim,A.Joachimiak,A.M.Edwards,X.Xu,M.Pennycooke,J.Gu,F.Cheu D.Christendat,Midwest Center For Structural Genomics (Mcsg)

Key ref:

Y.Kim et al. (2004). Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J Biol Chem, 279, 517-526. PubMed id: 14555659 DOI: 10.1074/jbc.M306054200

Date:

13-Mar-02 Release date: 21-Jan-03

Protein chains

Q9HLQ2  (PGP_THEAC) -  Phosphoglycolate phosphatase

Seq: 224 a.a.

Struc: 225 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.3.18 - Phosphoglycolate phosphatase.
• Reaction: 2-phosphoglycolate + H₂O = glycolate + phosphate

2-phosphoglycolate + H(2)O = glycolate (Bound ligand (Het Group name = FMT) matches with 60.00% similarity) + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (2 terms)
• Biochemical function: hydrolase activity (5 terms)

reference

DOI no: 10.1074/jbc.M306054200

J Biol Chem 279:517-526 (2004)

PubMed id: 14555659

Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.

Y.Kim, A.F.Yakunin, E.Kuznetsova, X.Xu, M.Pennycooke, J.Gu, F.Cheung, M.Proudfoot, C.H.Arrowsmith, A.Joachimiak, A.M.Edwards, D.Christendat.

ABSTRACT

The protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase.

Selected figure(s)

Figure 1.
FIG. 1. ClustalW alignment of proteins identified by a BLAST search of the National Center for Biotechnology Information (NCBI) sequence data base. The three conserved motifs, highlighted in black, are observed in proteins belonging to the HAD superfamily. TA, gi 16081332; TV, Thermoplasma volcanium gi 13541111; MT, M. thermoautotrophicum gi 7429215; CA, Clostridium acetobutylicum gi 15893986; MP, Mycoplasma pneumoniae gi 13508166; MC, Mycoplasma capricolum gi 602030.

Figure 3.
FIG. 3. A, C[ ]tracing showing the superposition of the structure of TA0175 with that of PSP (Protein Data Bank code 1f5s [PDB] ) showing conservation within the HAD domain and significant structural divergence within the cap domain. B, superposition of the two molecules of TA0175 to show regions with distinct conformational variations. Molecule A, including Ca^2+ and water molecules, is shown in red, and Molecule B is shown in dark green. Molecule A contains two Ca^2+ atoms in this region, while Molecule B has one Ca^2+, which is shifted 1.6 Å toward the second Ca^2+ of Molecule A. Overall the two molecules in the asymmetric unit superimpose with a root mean square deviation value of 0.52 Å with variations shown for loops L1 and L5. Some observable changes in amino acid positioning include Ser-175 of Molecule B, which shifted 1.3 Å toward a Ca^2+ of Molecule B to make a coordinated bond. Asp-174 of Molecule A is coordinated to both Ca^2+ atoms. The carbonyl of Gly-10 in molecule A is liganded to a Ca^2+, and in Molecule B the carboxylate group of Asp-10 is liganded to a Ca^2+. C, superposition of the active site of TA0175 with that of E. coli PSP. Most of the functional residues are conserved in primary amino acid sequence motifs and superpose in the tertiary structure as well, indicating a high level of conservation among this superfamily of proteins. The location of these active site residues and their interaction with Ca^2+ (blue, CA) for TA0175 is analogous to the interactions observed for Mg2+ (green, MG) in E. coli PSP and indicates that Mg2+ may form similar interactions in TA0175.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 517-526) copyright 2004.

Figures were selected by an automated process.