1HQ6

STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

pH-induced structural changes regulate histidine decarboxylase activity in Lactobacillus 30a.

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

(2001) J Mol Biol 306: 727-732

  • DOI: https://doi.org/10.1006/jmbi.2000.4430
  • Primary Citation of Related Structures:  
    1HQ6

  • PubMed Abstract: 

    Histidine decarboxylase (HDC) from Lactobacillus 30a produces histamine that is essential to counter waste acids, and to optimize cell growth. The HDC trimer is active at low pH and inactive at neutral to alkaline pH. We have solved the X-ray structure of HDC at pH 8 and revealed the novel mechanism of pH regulation. At high pH helix B is unwound, destroying the substrate binding pocket. At acid pH the helix is stabilized, partly through protonation of Asp198 and Asp53 on either side of the molecular interface, acting as a proton trap. In contrast to hemoglobin regulation, pH has a large effect on the tertiary structure of HDC monomers and relatively little or no effect on quaternary structure.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTIDINE DECARBOXYLASE
A, C
81Lactobacillus sp. 30AMutation(s): 0 
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
B, D
229Lactobacillus sp. 30AMutation(s): 1 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.263 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.431α = 90
b = 117.431β = 90
c = 241.6γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-21
    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: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations