2FPW

Crystal Structure of the N-terminal Domain of E.coli HisB- Phosphoaspartate intermediate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

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

(2006) J Biol Chem 281: 37930-37941

  • DOI: https://doi.org/10.1074/jbc.M604916200
  • Primary Citation of Related Structures:  
    2FPR, 2FPS, 2FPU, 2FPW, 2FPX

  • PubMed 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 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+).


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidine biosynthesis bifunctional protein hisB
A, B
176Escherichia coli O157:H7Mutation(s): 1 
Gene Names: hisBZ3184ECs2823
EC: 3.1.3.15 (PDB Primary Data), 4.2.1.19 (UniProt)
UniProt
Find proteins for Q9S5G5 (Escherichia coli O157:H7)
Explore Q9S5G5 
Go to UniProtKB:  Q9S5G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S5G5
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHD
Query on PHD
A, B
L-PEPTIDE LINKINGC4 H8 N O7 PASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.983α = 90
b = 132.408β = 90
c = 105.685γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description