1PYA

REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.

Gallagher, T.Rozwarski, D.A.Ernst, S.R.Hackert, M.L.

(1993) J.Mol.Biol. 230: 516-528

  • DOI: 10.1006/jmbi.1993.1168

  • PubMed Abstract: 
  • The crystal structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a has been refined to an R-value of 0.15 (for the 5.0 to 2.5 A resolution shell) and 0.17 (for the 10.0 to 2.5 A resolution shell). A description of the over ...

    The crystal structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a has been refined to an R-value of 0.15 (for the 5.0 to 2.5 A resolution shell) and 0.17 (for the 10.0 to 2.5 A resolution shell). A description of the overall structure is presented, focusing on secondary structure and subunit association. The enzyme is a hexamer of alpha beta subunits. Separate alpha and beta-chains arise from an autocatalytic cleavage reaction between two serine residues, which results in the pyruvoyl cofactor. The central core of the alpha beta subunit is a beta-sandwich which consists of two face-to-face three-stranded antiparallel beta-sheets, flanked by alpha-helices on each side. The beta-sandwich creates a stable fold that allows conformational strain to be introduced across an internal cleavage region between the alpha and beta chains and places the pyruvoyl cofactor in a position for efficient electron withdrawal from the substrate. Three alpha beta subunits are related by a molecular three-fold symmetry axis to form a trimer whose interfaces have complementary surfaces and extensive molecular interactions. Each of the interfaces contains an active site and a solvent channel that leads from the active site to the exterior of the molecule. The trimers are related by a crystallographic two-fold symmetry axis to form the hexamer with an overall dumbbell shape. The interface between trimers has few molecular interactions.


    Related Citations: 
    • Structure Determination of Histidine Decarboxylase from Lactobacillus 30A at 3.0 Angstroms Resolution
      Parks, E.H.,Ernst, S.R.,Hamlin, R.,Xuong, N.H.,Hackert, M.L.
      (1985) J.Mol.Biol. 182: 455
    • Pyruvoyl-Dependent Histidine Decarboxylase: Active Site Structure and Mechanistic Analysis
      Gallagher, T.,Snell, E.E.,Hackert, M.L.
      (1989) J.Biol.Chem. 264: 12737
    • The Molecular Symmetry of Histidine Decarboxylase and Prohistidine Decarboxylase by Rotation Function Analysis
      Parks, E.H.,Clinger, K.,Hackert, M.L.
      (1983) Acta Crystallogr.,Sect.B 39: 490
    • Crystallization and Subunit Structure of Histidine Decarboxylase from Lactobacillus 30A
      Hackert, M.L.,Meador, W.E.,Oliver, R.M.,Salmon, J.B.,Rescei, P.A.,Snell, E.E.
      (1981) J.Biol.Chem. 256: 687


    Organizational Affiliation

    Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
A, C, E
81Lactobacillus sp. (strain 30a)Gene Names: hdcA
EC: 4.1.1.22
Find proteins for P00862 (Lactobacillus sp. (strain 30a))
Go to UniProtKB:  P00862
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
B, D, F
229Lactobacillus sp. (strain 30a)Gene Names: hdcA
EC: 4.1.1.22
Find proteins for P00862 (Lactobacillus sp. (strain 30a))
Go to UniProtKB:  P00862
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PYR
Query on PYR
B, D, F
NON-POLYMERC3 H4 O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.150 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 221.700α = 90.00
b = 221.700β = 90.00
c = 107.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other