1HQ6 | pdb_00001hq6

STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 8

• PDB DOI: https://doi.org/10.2210/pdb1HQ6/pdb

• Classification: LYASE
• Organism(s): Lactobacillus sp. 30A
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-12-14 Released: 2001-03-21 
• Deposition Author(s): Schelp, E., Worley, S., Monzingo, A.F., Ernst, S., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.314 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Model: experimental

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 Biology 306: 727-732

• PubMed: 11243783 
• DOI: https://doi.org/10.1006/jmbi.2000.4430
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.27 kDa 
• Atom Count: 4,600 
• Modeled Residue Count: 590 
• Deposited Residue Count: 620 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTIDINE DECARBOXYLASE	A, C	81	Lactobacillus sp. 30A	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTIDINE DECARBOXYLASE	B, D	229	Lactobacillus sp. 30A	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.314 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.431	α = 90
b = 117.431	β = 90
c = 241.6	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-21 
Deposition Author(s): Schelp, E., Worley, S., Monzingo, A.F., Ernst, S., Robertus, J.D.

Revision History  

• 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
• Version 2.1: 2024-11-20
  Changes: Structure summary