3S0M | pdb_00003s0m

A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3S0M

This is version 1.2 of the entry. See complete history

Literature

A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.

Saylor, B.T.Reinhardt, L.A.Lu, Z.Shukla, M.S.Nguyen, L.Cleland, W.W.Angerhofer, A.Allen, K.N.Richards, N.G.

(2012) Biochemistry 51: 2911-2920

  • DOI: https://doi.org/10.1021/bi300001q
  • Primary Citation Related Structures: 
    3S0M

  • PubMed Abstract: 

    The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.


  • Organizational Affiliation
    • Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.

Macromolecule Content 

  • Total Structure Weight: 43.13 kDa 
  • Atom Count: 3,388 
  • Modeled Residue Count: 377 
  • Deposited Residue Count: 377 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxalate decarboxylase oxdC377Bacillus subtilisMutation(s): 1 
Gene Names: BSU33240oxalate decarboxylaseoxdCyvrK
EC: 4.1.1.2
UniProt
Find proteins for O34714 (Bacillus subtilis (strain 168))
Explore O34714 
Go to UniProtKB:  O34714
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34714
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
D [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
MN

Query on MN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.761α = 90
b = 154.761β = 90
c = 121.499γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
APEXdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.2: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations