PDBsum entry 2fpx

Hydrolase

PDB id: 2fpx

Contents

Protein chains

156 a.a. *

160 a.a. *

Ligands

SO4

Metals

_MG ×3

_ZN ×2

Waters ×513

* Residue conservation analysis

PDB id:

2fpx

Name:

Hydrolase

Title:

Crystal structure of the n-terminal domain of e.Coli hisb- sulfate complex.

Structure:

Histidine biosynthesis bifunctional protein hisb. Chain: a, b. Fragment: n-terminal domain, histidinol-phosphatase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83334. Strain: o157:h7. Gene: hisb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.179 R-free: 0.213

Authors:

E.S.Rangarajan,M.Cygler,A.Matte,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Key ref:

E.S.Rangarajan et al. (2006). Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway. J Biol Chem, 281, 37930-37941. PubMed id: 16966333 DOI: 10.1074/jbc.M604916200

Date:

17-Jan-06 Release date: 05-Sep-06

Protein chain

Q9S5G5  (HIS7_ECO57) -  Histidine biosynthesis bifunctional protein HisB from Escherichia coli O157:H7

Seq: 355 a.a.

Struc: 156 a.a.

Protein chain

Q9S5G5  (HIS7_ECO57) -  Histidine biosynthesis bifunctional protein HisB from Escherichia coli O157:H7

Seq: 355 a.a.

Struc: 160 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.3.1.3.15 - histidinol-phosphatase.
• Pathway: Histidine Biosynthesis (late stages)
• Reaction: L-histidinol phosphate + H2O = L-histidinol + phosphate
• Enzyme class 2: Chains A, B: E.C.4.2.1.19 - imidazoleglycerol-phosphate dehydratase.

Pathway:

• Reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2- oxopropyl phosphate + H2O

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M604916200

J Biol Chem 281:37930-37941 (2006)

PubMed id: 16966333

Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway.

E.S.Rangarajan, A.Proteau, J.Wagner, M.N.Hung, A.Matte, M.Cygler.

ABSTRACT

HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of l-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. HisB-N forms dimers in the crystal and in solution. The structure shows the presence of a structural Zn(2+) ion stabilizing the conformation of an extended loop. Two metal binding sites were also identified in the active site. Their presence was further confirmed by isothermal titration calorimetry. HisB-N is active in the presence of Mg(2+), Mn(2+), Co(2+), or Zn(2+), but Ca(2+) has an inhibitory effect. We have determined structures of several intermediate states corresponding to snapshots along the reaction pathway, including that of the phosphoaspartate intermediate. A catalytic mechanism, different from that described for other HAD enzymes, is proposed requiring the presence of the second metal ion not found in the active sites of previously characterized HAD enzymes, to complete the second half-reaction. The proposed mechanism is reminiscent of two-Mg(2+) ion catalysis utilized by DNA and RNA polymerases and many nucleases. The structure also provides an explanation for the inhibitory effect of Ca(2+).

Selected figure(s)

Figure 5.
FIGURE 5. a, states along the reaction pathway based on determined structures. I, the initial state with site 1 occupied by Mg^2+; II, HisB-N with histidinol phosphate substrate modeled on the structure of histidinol complex; III, phosphoaspartate intermediate with Mg^2+ occupying sites 1 and 2; IV, release of phosphate and Mg^2+ from site 2; b, superposition of the active site residues of HisB-N (gray) with E. coli AphA (orange). Red spheres represent water molecules; violet spheres show metal binding sites. The orientations of Asp^12 and its equivalent in AphA are different. Asp^12 is stabilized by hydrogen bonds (blue) to Arg^11, site 2, and bridging water W4. Asp^46 of AphA is hydrogen-bonded (orange) to Arg^114, approaching from the opposite direction to Arg^11 of HisB-N, and to the of phosphate oxygen in the position of water W1. Only HisB residues are labeled.

Figure 6.
FIGURE 6. Changes in the HisB-N substrate binding region along the reaction pathway shown in a surface representation. The residues that undergo conformational changes due to binding of the substrate and/or metal ions, namely Glu^18, Phe^23, and Arg^132 are shown as sticks under semitransparent surface. All structures are shown in the same orientation. a, HisB-N·Mg; b, HisB-N·Mg/histidinol; c, HisB-N·Ca/pAsp; and d, HisB-N·Mg/sulfate.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 37930-37941) copyright 2006.

Figures were selected by an automated process.