1GKM

HISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED WITH L-CYSTEINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Two Histidine Ammonia-Lyase Modifications and Implications for the Catalytic Mechanism

Baedeker, M.Schulz, G.E.

(2002) Eur.J.Biochem. 269: 1790

  • Primary Citation of Related Structures:  1GKJ

  • PubMed Abstract: 
  • Histidine ammonia-lyase (EC 4.3.1.3) catalyzes the nonoxidative elimination of the alpha-amino group of histidine using a 4-methylidene-imidazole-5-one (MIO), which is formed autocatalytically from the internal peptide segment 142Ala-Ser-Gly. The str ...

    Histidine ammonia-lyase (EC 4.3.1.3) catalyzes the nonoxidative elimination of the alpha-amino group of histidine using a 4-methylidene-imidazole-5-one (MIO), which is formed autocatalytically from the internal peptide segment 142Ala-Ser-Gly. The structure of the enzyme inhibited by a reaction with l-cysteine was established at the very high resolution of 1.0 A. Five active center mutants were produced and their catalytic activities were measured. Among them, mutant Tyr280-->Phe could be crystallized and its structure could be determined at 1.7 A resolution. It contains a planar sp2-hybridized 144-N atom of MIO, in contrast to the pyramidal sp3-hybridized 144-N of the wild-type. With the planar 144-N atom, MIO assumes the conformation of a putative intermediate aromatic state of the reaction, demonstrating that the conformational barrier between aromatic and wild-type states is very low. The data led to a new proposal for the geometry for the catalyzed reaction, which also applies to the closely related phenylalanine ammonia-lyase (EC 4.3.1.5). Moreover, it suggested an intermediate binding site for the released ammonia.


    Related Citations: 
    • Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile
      Schwede, T.F.,Retey, J.,Schulz, G.E.
      (1999) Biochemistry 38: 5355
    • Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue
      Schwede, T.F.,Baedeker, M.,Langer, M.,Retey, J.,Schulz, G.E.
      (1999) Protein Eng. 12: 151


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTIDINE AMMONIA-LYASE
A
509Pseudomonas putidaGene Names: hutH
EC: 4.3.1.3
Find proteins for P21310 (Pseudomonas putida)
Go to UniProtKB:  P21310
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

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Download CCD File 
A
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
CYS
Query on CYS

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Download CCD File 
A
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MDO
Query on MDO
A
L-PEPTIDE LINKINGC8 H11 N3 O3ALA, SER, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.135 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.267α = 90.00
b = 116.788β = 90.00
c = 129.532γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SHELXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-05
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance