2V5K | pdb_00002v5k

Class II aldolase HpcH - magnesium - oxamate complex

• PDB DOI: https://doi.org/10.2210/pdb2V5K/pdb

• Classification: LYASE
• Organism(s): Escherichia coli C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-06 Released: 2007-10-02 
• Deposition Author(s): Rea, D., Fulop, V., Bugg, T.D.H., Roper, D.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.192 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanism of Hpch: A Metal Ion Dependent Class II Aldolase from the Homoprotocatechuate Degradation Pathway of Escherichia Coli.

Rea, D., Fulop, V., Bugg, T.D.H., Roper, D.I.

(2007) J Mol Biology 373: 866

• PubMed: 17881002 
• DOI: https://doi.org/10.1016/j.jmb.2007.06.048
• Primary Citation Related Structures: 
  2V5J, 2V5K


• PubMed Abstract: 
  

  Microorganisms are adept at degrading chemically resistant aromatic compounds. One of the longest and most well characterized aromatic catabolic pathways is the 4-hydroxyphenylacetic acid degradation pathway of Escherichia coli. The final step involves the conversion of 4-hydroxy-2-oxo-heptane-1,7-dioate into pyruvate and succinic semialdehyde. This reaction is catalyzed by 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (HpcH), a member of the divalent metal ion dependent class II aldolase enzymes that have great biosynthetic potential. We have solved the crystal structure of HpcH in the apo form, and with magnesium and the substrate analogue oxamate bound, to 1.6 A and 2.0 A, respectively. Comparison with similar structures of the homologous 2-dehydro-3-deoxygalactarate aldolase, coupled with site-directed mutagenesis data, implicate histidine 45 and arginine 70 as key catalytic residues.

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Organizational Affiliation: 
• Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 62.69 kDa 
• Atom Count: 4,264 
• Modeled Residue Count: 522 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE	A, B	287	Escherichia coli C	Mutation(s): 0  EC: 4.1.2 (PDB Primary Data), 4.1.2.52 (UniProt)
UniProt
Find proteins for Q47098 (Escherichia coli) Explore Q47098  Go to UniProtKB:  Q47098

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXM	D [auth A], G [auth B]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.192 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.2	α = 90
b = 152.2	β = 90
c = 152.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Rea, D., Fulop, V., Bugg, T.D.H., Roper, D.I.

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description