3QVA | pdb_00003qva

Structure of Klebsiella pneumoniae 5-hydroxyisourate hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3QVA/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-02-25 Released: 2011-08-24 
• Deposition Author(s): French, J.B., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae.

French, J.B., Ealick, S.E.

(2011) Acta Crystallogr D Biol Crystallogr 67: 671-677

• PubMed: 21795808 
• DOI: https://doi.org/10.1107/S090744491101746X
• Primary Citation Related Structures: 
  3QVA


• PubMed Abstract: 
  

  The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined. KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional roles of the active-site residues. Based upon the structural and kinetic data, a mechanism is proposed for the KpHIUH-catalyzed reaction.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 49.96 kDa 
• Atom Count: 3,454 
• Modeled Residue Count: 422 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin-like protein	A, B, C, D	116	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: HpxT, KPN78578_16360, KPN_01666 EC: 3.5.2.17
UniProt
Find proteins for A6T926 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T926  Go to UniProtKB:  A6T926

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth C], F [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.192	α = 90
b = 101.302	β = 90
c = 106.111	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): French, J.B., Ealick, S.E.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations