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: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  1IBT, 1IBU, 1IBV

  • 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 alka ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTIDINE DECARBOXYLASE BETA CHAIN
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
HISTIDINE DECARBOXYLASE ALPHA CHAIN
B, D, F
228Lactobacillus 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
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVH
Query on PVH

Download SDF File 
Download CCD File 
B, D, F
HISTIDINE-METHYL-ESTER
C7 H12 N3 O2
BXRMEWOQUXOLDH-LURJTMIESA-O
 Ligand Interaction
PYR
Query on PYR

Download SDF File 
Download CCD File 
B, D, F
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 97.017α = 90.00
b = 117.768β = 90.00
c = 205.789γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance