1GKM | pdb_00001gkm

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

• PDB DOI: https://doi.org/10.2210/pdb1GKM/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-08-16 Released: 2002-04-05 
• Deposition Author(s): Baedeker, M., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.135 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.227 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

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

• PubMed: 11895450 
• DOI: https://doi.org/10.1046/j.1432-1327.2002.02827.x
• Primary Citation Related Structures: 
  1GKJ, 1GKM


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.94 kDa 
• Atom Count: 4,360 
• Modeled Residue Count: 507 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine ammonia-lyase	A [auth B]	507	Pseudomonas putida	Mutation(s): 0  Gene Names: hutH EC: 4.3.1.3
UniProt
Find proteins for P21310 (Pseudomonas putida) Explore P21310  Go to UniProtKB:  P21310

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	B	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ZRF	A [auth B]	L-PEPTIDE LINKING	C8 H11 N3 O4		ALA, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.135 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.227 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.267	α = 90
b = 116.788	β = 90
c = 129.532	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-05 
Deposition Author(s): Baedeker, M., Schulz, G.E.

Revision History  

• Version 1.0: 2002-04-05
  Type: Initial release
  
• Version 1.1: 2011-09-07
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.3: 2019-10-23
  Changes: Data collection, Database references, Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2024-06-26
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2025-10-01
  Changes: Derived calculations, Structure summary