6INC | pdb_00006inc

Crystal structure of an acetolactate decarboxylase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6INC/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-24 Released: 2019-01-16 
• Deposition Author(s): Wu, W., Zhang, Q., Bartlam, M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae

Wu, W., Zhao, Q., Che, S., Jia, H., Liang, H., Zhang, H., Liu, R., Zhang, Q., Bartlam, M.

(2019) Biochem Biophys Res Commun 509: 154-160

• PubMed: 30580999 
• DOI: https://doi.org/10.1016/j.bbrc.2018.12.094
• Primary Citation Related Structures: 
  6INB, 6INC


• PubMed Abstract: 
  

  Acetolactate decarboxylase (ALDC) is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin), an important physiological metabolite excreted by microbes. Although the enzyme is widely present in microorganisms, few atomic structures and functions of ALDC have been reported to date. Here we report the crystal structure of ALDC from Klebsiella pneumoniae KP (KpALDC). KpALDC crystallizes in space group P3 ₁ 21 with one monomer per asymmetric unit. Analytical ultracentrifugation data shows that KpALDC forms a stable dimer but can exist as a tetramer in solution. A Zn ²⁺ ion is coordinated by three strictly-conserved histidines (His198, His200 and His211) and a conserved glutamate (Glu69), but the C-terminal tail that forms part of the active site in ALDC enzymes is disordered. A complex structure with ethane-1,2-diol shows a unusual mode of binding, whereby the ligand does not coordinate the Zn ²⁺ ion. MicroScale Thermophoresis analysis shows that KpALDC binds Zn ²⁺ ions, but no binding of Mg ²⁺ , Ca ²⁺ and Mn ²⁺ ions was detected.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China.
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China. Electronic address: [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 29.51 kDa 
• Atom Count: 2,015 
• Modeled Residue Count: 218 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-acetolactate decarboxylase	A	259	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: budA, BN49_3166 EC: 4.1.1.5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.152	α = 90
b = 55.152	β = 90
c = 119.377	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Wu, W., Zhang, Q., Bartlam, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570128

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description