1EB4

Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Autocatalytic Peptide Cyclization During Chain Folding of Histidine Ammonia-Lyase.

Baedeker, M.Schulz, G.E.

(2002) Structure 10: 61

  • DOI: 10.1016/s0969-2126(01)00692-x
  • Primary Citation of Related Structures:  
    1EB4, 1GK2, 1GK3

  • PubMed Abstract: 
  • Histidine ammonia-lyase requires a 4-methylidene-imidazole-5-one group (MIO) that is produced autocatalytically by a cyclization and dehydration step in a 3-residue loop of the polypeptide. The crystal structures of three mutants have been established. Two mutants were inactive and failed to form MIO, but remained unchanged elsewhere ...

    Histidine ammonia-lyase requires a 4-methylidene-imidazole-5-one group (MIO) that is produced autocatalytically by a cyclization and dehydration step in a 3-residue loop of the polypeptide. The crystal structures of three mutants have been established. Two mutants were inactive and failed to form MIO, but remained unchanged elsewhere. The third mutant showed very low activity and formed MIO, although it differed from an MIO-less mutant only by an additional 329-C(beta) atom. This atom forms one constraint during MIO formation, the other being the strongly connected Asp145. An exploration of the conformational space of the MIO-forming loop showed that the cyclization is probably enforced by a mechanic compression in a late stage of chain folding and is catalyzed by a well-connected internal water molecule. The cyclization of the respective 3-residue loop of green fluorescent protein is likely to occur in a similar reaction.


    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, D-79104 Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTIDINE AMMONIA-LYASEA507Pseudomonas putidaMutation(s): 3 
Gene Names: hutH
EC: 4.3.1.3
UniProt
Find proteins for P21310 (Pseudomonas putida)
Explore P21310 
Go to UniProtKB:  P21310
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MDO
Query on MDO
AL-PEPTIDE LINKINGC8 H11 N3 O3ALA, SER, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Observed: 0.171 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.97α = 90
b = 116.9β = 90
c = 129.31γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-21
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-05-30
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other