1IBW

STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT 25 C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.211 

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This is version 3.0 of the entry. See complete history


Literature

Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a.

Worley, S.Schelp, E.Monzingo, A.F.Ernst, S.Robertus, J.D.

(2002) Proteins 46: 321-329

  • DOI: https://doi.org/10.1002/prot.10042
  • Primary Citation of Related Structures:  
    1IBT, 1IBU, 1IBV, 1IBW

  • PubMed Abstract: 

    Histidine decarboxylase (HDC) from Lactobacillus 30a converts histidine to histamine, a process that enables the bacteria to maintain the optimum pH range for cell growth. HDC is regulated by pH; it is active at low pH and inactive at neutral to alkaline pH. The X-ray structure of HDC at pH 8 revealed that a helix was disordered, resulting in the disruption of the substrate-binding site. The HDC trimer has also been shown to exhibit cooperative kinetics at neutral pH, that is, histidine can trigger a T-state to R-state transition. The D53,54N mutant of HDC has an elevated Km, even at low pH, indicating that the enzyme assumes the low activity T-state. We have solved the structures of the D53,54N mutant at low pH, with and without the substrate analog histidine methyl ester (HME) bound. Structural analysis shows that the apo-D53,54N mutant is in the inactive or T-state and that binding of the substrate analog induces the enzyme to adopt the active or R-state. A mechanism for the cooperative transition is proposed.


  • Organizational Affiliation

    Institute of Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTIDINE DECARBOXYLASE BETA CHAIN
A, C, E
81Lactobacillus sp. 30AMutation(s): 2 
Gene Names: HDCA
EC: 4.1.1.22
UniProt
Find proteins for P00862 (Lactobacillus sp. (strain 30a))
Explore P00862 
Go to UniProtKB:  P00862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00862
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine decarboxylase alpha chain
B, D, F
229Lactobacillus sp. 30AMutation(s): 0 
Gene Names: hdcA
UniProt
Find proteins for P00862 (Lactobacillus sp. (strain 30a))
Explore P00862 
Go to UniProtKB:  P00862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00862
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.017α = 90
b = 117.768β = 90
c = 205.789γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-09
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.0: 2024-02-14
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary