PDBsum entry 2rb5

Unknown function

PDB id: 2rb5

Contents

Protein chain

261 a.a. *

Ligands

WO6

Metals

_MG

Waters ×501

* Residue conservation analysis

PDB id:

2rb5

Name:

Unknown function

Title:

X-ray crystallographic structures show conservation of a trigonal- bipyramidal intermediate in a phosphoryl-transfer superfamily.

Structure:

Putative uncharacterized protein. Chain: a. Engineered: yes

Source:

Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482. Gene: bacteroides thetaiotaomicron. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.03Å R-factor: 0.112 R-free: 0.136

Authors:

Z.Lu,D.Dunaway-Mariano,K.N.Allen

Key ref:

Z.Lu et al. (2008). The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state. Proc Natl Acad Sci U S A, 105, 5687-5692. PubMed id: 18398008 DOI: 10.1073/pnas.0710800105

Date:

18-Sep-07 Release date: 22-Apr-08

Protein chain

Q8A090  (Q8A090_BACTN) -  Haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)

Seq: 261 a.a.

Struc: 261 a.a.

DOI no: 10.1073/pnas.0710800105

Proc Natl Acad Sci U S A 105:5687-5692 (2008)

PubMed id: 18398008

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.

Z.Lu, D.Dunaway-Mariano, K.N.Allen.

ABSTRACT

The evolution of new catalytic activities and specificities within an enzyme superfamily requires the exploration of sequence space for adaptation to a new substrate with retention of those elements required to stabilize key intermediates/transition states. Here, we propose that core residues in the large enzyme family, the haloalkanoic acid dehalogenase enzyme superfamily (HADSF) form a "mold" in which the trigonal bipyramidal transition states formed during phosphoryl transfer are stabilized by electrostatic forces. The vanadate complex of the hexose phosphate phosphatase BT4131 from Bacteroides thetaiotaomicron VPI-5482 (HPP) determined at 1.00 A resolution via X-ray crystallography assumes a trigonal bipyramidal coordination geometry with the nucleophilic Asp-8 and one oxygen ligand at the apical position. Remarkably, the tungstate in the complex determined to 1.03 A resolution assumes the same coordination geometry. The contribution of the general acid/base residue Asp-10 in the stabilization of the trigonal bipyramidal species via hydrogen-bond formation with the apical oxygen atom is evidenced by the 1.52 A structure of the D10A mutant bound to vanadate. This structure shows a collapse of the trigonal bipyramidal geometry with displacement of the water molecule formerly occupying the apical position. Furthermore, the 1.07 A resolution structure of the D10A mutant complexed with tungstate shows the tungstate to be in a typical "phosphate-like" tetrahedral configuration. The analysis of 12 liganded HADSF structures deposited in the protein data bank (PDB) identified stringently conserved elements that stabilize the trigonal bipyramidal transition states by engaging in favorable electrostatic interactions with the axial and equatorial atoms of the transferring phosphoryl group.

Selected figure(s)

Figure 1.
The general catalytic mechanism for phosphohydrolase members of the HAD superfamily. Catalysis proceeds through an aspartylphosphate intermediate.

Figure 4.
The HPP-D10A active site in the presence of phosphate mimics and the cofactor Mg^2+ (magenta sphere). The 2Fo-Fc composite-omit electron density maps (gray cages) are contoured at 1.5σ. (A) The 1.52 Å resolution structure of HPP-D10A complexed with vanadate. Bond angles are O1-V-O2, 111.6°; O2-V-O3, 122.9°; O1-V-O3, 117.7°; O1-V-OAsp8, 95.2°; O2-V-OAsp8, 100.1°; O3-V-OAsp8, 102.3°. (B) The 1.07 Å resolution structure of HPP-D10A complexed with tungstate. Bond angles are O1-W-O2, 112.8°; O2-W-O3, 118.8°; O1-W-O3, 112.3°; O1-W-O4, 103.8°; O2-W-O4, 104.1°; O3-W-O4, 102.9°{ideal bond angles tungstate [PDB accession code 1FR3 (32)] O1-W-O2, 111.1°; O2-W-O3, 111.1°; O1-W-O3, 108.2°; O1-W-O4, 107.7°; O2-W-O4, 111.3°; O3-W-O4, 107.6°}. The water molecules are depicted as red spheres.

Figures were selected by an automated process.