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The Structure of Oxalate Decarboxylase at its Active pH

https://doi.org/10.1101/426874
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Hydrogen Bond in the Solid State
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Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
inferredcites →https://doi.org/10.1002/prot.20016openalex-snapshot
Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 Å resolution
inferredcites →https://doi.org/10.1002/prot.22927openalex-snapshot
Salt bridges: Geometrically specific, designable interactions
inferredcites →https://doi.org/10.1006/jmbi.1995.0653openalex-snapshot
Complex Salt Bridges in Proteins: Statistical Analysis of Structure and Function
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Anatomy of hot spots in protein interfaces
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Salt bridge stability in monomeric proteins 1 1Edited by J. M. Thornton
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Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/0-306-46883-2_8openalex-snapshot
Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function
inferredcites →https://doi.org/10.1007/s00894-015-2882-zopenalex-snapshot
Theoretical study of the cooperative effects between the triel bond and the pnicogen bond in BF3···NCXH2···Y (X = P, As, Sb; Y = H2O, NH3) complexes
inferredcites →https://doi.org/10.1007/s00894-016-3075-0openalex-snapshot
Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study
inferredcites →https://doi.org/10.1007/s00894-016-3195-6openalex-snapshot
DFT and TDDFT investigation of the Schiff base formed by tacrine and saccharin
inferredcites →https://doi.org/10.1007/s00894-017-3376-yopenalex-snapshot
Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions
inferredcites →https://doi.org/10.1016/0003-9861(64)90040-2openalex-snapshot
Enzymatic oxalate decarboxylation in Aspergillus niger
inferredcites →https://doi.org/10.1016/0003-9861(65)90355-3openalex-snapshot
An oxalic acid decarboxylase of Myrothecium verrucaria
inferredcites →https://doi.org/10.1016/0079-6107(84)90007-5openalex-snapshot
Hydrogen bonding in globular proteins
inferredcites →https://doi.org/10.1016/j.abb.2004.08.032openalex-snapshot
The enzymes of oxalate metabolism: unexpected structures and mechanisms
inferredcites →https://doi.org/10.1016/j.abb.2007.03.016openalex-snapshot
Investigating the roles of putative active site residues in the oxalate decarboxylase from Bacillus subtilis
inferredcites →https://doi.org/10.1016/j.bbapap.2006.08.007openalex-snapshot
Modeling electrostatic effects in proteins
inferredcites →https://doi.org/10.1016/j.biotechadv.2012.02.002openalex-snapshot
Software tools for identification, visualization and analysis of protein tunnels and channels
inferredcites →https://doi.org/10.1016/j.cplett.2004.06.011openalex-snapshot
A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
inferredcites →https://doi.org/10.1016/j.freeradbiomed.2011.01.023openalex-snapshot
EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction
inferredcites →https://doi.org/10.1016/j.freeradbiomed.2014.12.012openalex-snapshot
Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4
inferredcites →https://doi.org/10.1016/j.sbi.2010.09.005openalex-snapshot
A role for flexible loops in enzyme catalysis
inferredcites →https://doi.org/10.1016/s0021-9258(18)66022-3openalex-snapshot
ENZYMATIC DECARBOXYLATION OF MALONIC ACID
inferredcites →https://doi.org/10.1016/s0021-9258(19)50807-9openalex-snapshot
ENZYMATIC DECARBOXYLATION OF OXALIC ACID
inferredcites →https://doi.org/10.1021/acs.biochem.6b00043openalex-snapshot
Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase
inferredcites →https://doi.org/10.1021/acs.biochem.6b00891openalex-snapshot
Redox Cycling, pH Dependence, and Ligand Effects of Mn(III) in Oxalate Decarboxylase fromBacillus subtilis
inferredcites →https://doi.org/10.1021/bi0200965openalex-snapshot
Structure of Oxalate Decarboxylase from Bacillus subtilis at 1.75 Å Resolution ,
inferredcites →https://doi.org/10.1021/bi300001qopenalex-snapshot
A Structural Element That Facilitates Proton-Coupled Electron Transfer in Oxalate Decarboxylase
inferredcites →https://doi.org/10.1021/bi700947sopenalex-snapshot
Oxalate Decarboxylase and Oxalate Oxidase Activities Can Be Interchanged with a Specificity Switch of up to 282 000 by Mutating an Active Site Lid,
inferredcites →https://doi.org/10.1021/bi801856kopenalex-snapshot
Metal Dependence of Oxalate Decarboxylase Activity
inferredcites →https://doi.org/10.1021/ed200202ropenalex-snapshot
The Oxalate Dianion, C2O42–: Planar or Nonplanar?
inferredcites →https://doi.org/10.1021/ja0286977openalex-snapshot
Heavy Atom Isotope Effects on the Reaction Catalyzed by the Oxalate Decarboxylase from Bacillus subtilis
inferredcites →https://doi.org/10.1021/ja408138fopenalex-snapshot
Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations
inferredcites →https://doi.org/10.1021/jp0715326openalex-snapshot
Multifrequency EPR Studies on the Mn(II) Centers of Oxalate Decarboxylase
inferredcites →https://doi.org/10.1023/a:1008781006867openalex-snapshot
Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
inferredcites →https://doi.org/10.1038/nchem.2643openalex-snapshot
Why copper is preferred over iron for oxygen activation and reduction in haem-copper oxidases
inferredcites →https://doi.org/10.1039/c5cp06638gopenalex-snapshot
A density functional theory protocol for the calculation of redox potentials of copper complexes
inferredcites →https://doi.org/10.1042/bj20070708openalex-snapshot
The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations
inferredcites →https://doi.org/10.1042/ebc20160070openalex-snapshot
Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes
inferredcites →https://doi.org/10.1063/1.456153openalex-snapshot
Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen
inferredcites →https://doi.org/10.1073/pnas.0805364105openalex-snapshot
Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection
inferredcites →https://doi.org/10.1074/jbc.m107202200openalex-snapshot
Oxalate Decarboxylase Requires Manganese and Dioxygen for Activity
inferredcites →https://doi.org/10.1074/jbc.m313820200openalex-snapshot
A Closed Conformation of Bacillus subtilis Oxalate Decarboxylase OxdC Provides Evidence for the True Identity of the Active Site
inferredcites →https://doi.org/10.1093/nar/gkq471openalex-snapshot
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions
inferredcites →https://doi.org/10.1093/oxfordjournals.jbchem.a126533openalex-snapshot
OXALIC ACID DECARBOXYLASE, A NEW ENZYME FROM THE MYCELIUM OF WOOD DESTROYING FUNGI
inferredcites →https://doi.org/10.1107/s0021889807021206openalex-snapshot
Phaser crystallographic software
inferredcites →https://doi.org/10.1107/s0907444904019158openalex-snapshot
Coot : model-building tools for molecular graphics
inferredcites →https://doi.org/10.1107/s0907444909047337openalex-snapshot
XDS
inferredcites →https://doi.org/10.1107/s0907444909052925openalex-snapshot
PHENIX : a comprehensive Python-based system for macromolecular structure solution
inferredcites →https://doi.org/10.1128/jb.182.18.5271-5273.2000openalex-snapshot
Bacillus subtilis YvrK Is an Acid-Induced Oxalate Decarboxylase
inferredcites →https://doi.org/10.1371/journal.pcbi.1002708openalex-snapshot
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/pro.4537openalex-snapshot
Selective incorporation of 5‐hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.138764openalex-snapshot
Enzymatic and structural properties of a novel oxalate decarboxylase BsOxdC from Bacillus safensis and its potential pH-dependent catalytic mechanism
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.145834openalex-snapshot
Enzymatic characterization, surface display, and application of Dichomitus squalens oxalate decarboxylase to enhance nutritional quality of wheat germ
inferred← citeshttps://doi.org/10.1016/j.jbc.2021.100857openalex-snapshot
Oxalate decarboxylase uses electron hole hopping for catalysis
inferred← citeshttps://doi.org/10.1021/acs.jafc.4c00172openalex-snapshot
Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation
inferred← citeshttps://doi.org/10.1080/07391102.2021.2024882openalex-snapshot
Molecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12
inferred← citeshttps://doi.org/10.3390/molecules29184414openalex-snapshot
Bidentate Substrate Binding Mode in Oxalate Decarboxylase
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