1OZG

The crystal structure of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structures of Klebsiella pneumoniae Acetolactate Synthase with Enzyme-bound Cofactor and with an Unusual Intermediate.

Pang, S.S.Duggleby, R.G.Schowen, R.L.Guddat, L.W.

(2004) J.Biol.Chem. 279: 2242-2253

  • DOI: 10.1074/jbc.M304038200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acetohydroxyacid synthase (AHAS) and acetolactate synthase (ALS) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the decarboxylation of pyruvate to give a cofactor-bound hydroxyethyl group, which is transferred to a second molecule of ...

    Acetohydroxyacid synthase (AHAS) and acetolactate synthase (ALS) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the decarboxylation of pyruvate to give a cofactor-bound hydroxyethyl group, which is transferred to a second molecule of pyruvate to give 2-acetolactate. AHAS is found in plants, fungi, and bacteria, is involved in the biosynthesis of the branched-chain amino acids, and contains non-catalytic FAD. ALS is found only in some bacteria, is a catabolic enzyme required for the butanediol fermentation, and does not contain FAD. Here we report the 2.3-A crystal structure of Klebsiella pneumoniae ALS. The overall structure is similar to AHAS except for a groove that accommodates FAD in AHAS, which is filled with amino acid side chains in ALS. The ThDP cofactor has an unusual conformation that is unprecedented among the 26 known three-dimensional structures of nine ThDP-dependent enzymes, including AHAS. This conformation suggests a novel mechanism for ALS. A second structure, at 2.0 A, is described in which the enzyme is trapped halfway through the catalytic cycle so that it contains the hydroxyethyl intermediate bound to ThDP. The cofactor has a tricyclic structure that has not been observed previously in any ThDP-dependent enzyme, although similar structures are well known for free thiamine. This structure is consistent with our proposed mechanism and probably results from an intramolecular proton transfer within a tricyclic carbanion that is the true reaction intermediate. Modeling of the second molecule of pyruvate into the active site of the enzyme with the bound intermediate is consistent with the stereochemistry and specificity of ALS.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, the University of Queensland, Brisbane, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetolactate synthase, catabolic
A, B
566Klebsiella pneumoniaeMutation(s): 0 
Gene Names: budB (ilvK)
EC: 2.2.1.6
Find proteins for P27696 (Klebsiella pneumoniae)
Go to UniProtKB:  P27696
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HE3
Query on HE3

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A, B
2-HYDROXYETHYL DIHYDROTHIACHROME DIPHOSPHATE
2-{(9AS)-9A-[(1S)-1-HYDROXYETHYL]-2,7-DIMETHYL-9A,10-DIHYDRO-5H-PYRIMIDO[4,5-D][1,3]THIAZOLO[3,2-A]PYRIMIDIN-8-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
C14 H22 N4 O8 P2 S
UQFVHIGKDHNMJT-XPTSAGLGSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.488α = 90.00
b = 160.561β = 90.00
c = 129.454γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance