OxdC

• Description: oxalate decarboxylase
  
  

Gene name	oxdC
Synonyms	yvrK
Essential	no
Product	oxalate decarboxylase
Function	unknown
Gene expression levels in SubtiExpress: oxdC
MW, pI	43 kDa, 5.101
Gene length, protein length	1155 bp, 385 aa
Immediate neighbours	yvrJ, yvrL
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

acid stress proteins (controlled by YvrI-YvrHa), phosphoproteins

This gene is a member of the following regulons

YvrI-YvrHa regulon

The gene

Basic information

• Locus tag: BSU33240

Database entries

• BsubCyc: BSU33240

• DBTBS entry: no entry

• SubtiList entry: [1]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: Oxalate = formate + CO₂ (according to Swiss-Prot)

• Protein family:

• Paralogous protein(s): OxdD

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:
  • phosphorylated on Arg-12 PubMed

• Cofactors:
  • requires two Mn(II) centers for activity PubMed

• Effectors of protein activity:

• Interactions:

• Localization: cytoplasm (according to Swiss-Prot)

Database entries

• BsubCyc: BSU33240

• Structure: 1UW8

• UniProt: O34714

• KEGG entry: [2]

• E.C. number: 4.1.1.2

Expression and regulation

• Operon: oxdC-yvrL PubMed

• Expression browser: oxdC PubMed

• Sigma factor: YvrI-YvrHa PubMed

• Regulation: induced by acidic growth conditions PubMed

• Regulatory mechanism:

• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 193 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 4306 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2602 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 4926 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

Labs working on this gene/protein

John Helmann, Cornell University, USA Homepage

References

Reviews

Miia R Mäkelä, Kristiina Hildén, Taina K Lundell
Oxalate decarboxylase: biotechnological update and prevalence of the enzyme in filamentous fungi.
Appl Microbiol Biotechnol: 2010, 87(3);801-14
[PubMed:20464388] [WorldCat.org] [DOI] (I p)

Original publications

Eunhye Lee, Byong Chang Jeong, Yong Hyun Park, Hyeon Hoe Kim
Expression of the gene encoding oxalate decarboxylase from Bacillus subtilis and characterization of the recombinant enzyme.
BMC Res Notes: 2014, 7;598
[PubMed:25186982] [WorldCat.org] [DOI] (I e)

Pablo Campomanes, Whitney F Kellett, Lindsey M Easthon, Andrew Ozarowski, Karen N Allen, Alexander Angerhofer, Ursula Rothlisberger, Nigel G J Richards
Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations.
J Am Chem Soc: 2014, 136(6);2313-23
[PubMed:24444454] [WorldCat.org] [DOI] (I p)

K Anbazhagan, P Sasikumar, S Gomathi, H P Priya, G S Selvam
In vitro degradation of oxalate by recombinant Lactobacillus plantarum expressing heterologous oxalate decarboxylase.
J Appl Microbiol: 2013, 115(3);880-7
[PubMed:23734819] [WorldCat.org] [DOI] (I p)

Alexander K W Elsholz, Kürsad Turgay, Stephan Michalik, Bernd Hessling, Katrin Gronau, Dan Oertel, Ulrike Mäder, Jörg Bernhardt, Dörte Becher, Michael Hecker, Ulf Gerth
Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis.
Proc Natl Acad Sci U S A: 2012, 109(19);7451-6
[PubMed:22517742] [WorldCat.org] [DOI] (I p)

Benjamin T Saylor, Laurie A Reinhardt, Zhibing Lu, Mithila S Shukla, Linda Nguyen, W Wallace Cleland, Alexander Angerhofer, Karen N Allen, Nigel G J Richards
A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.
Biochemistry: 2012, 51(13);2911-20
[PubMed:22404040] [WorldCat.org] [DOI] (I p)

Mario E G Moral, Chingkuang Tu, Nigel G J Richards, David N Silverman
Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases.
Anal Biochem: 2011, 418(1);73-7
[PubMed:21782782] [WorldCat.org] [DOI] (I p)

Witcha Imaram, Benjamin T Saylor, Christopher P Centonze, Nigel G J Richards, Alexander Angerhofer
EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction.
Free Radic Biol Med: 2011, 50(8);1009-15
[PubMed:21277974] [WorldCat.org] [DOI] (I p)

Mario E G Moral, Chingkuang Tu, Witcha Imaram, Alexander Angerhofer, David N Silverman, Nigel G J Richards
Nitric oxide reversibly inhibits Bacillus subtilis oxalate decarboxylase.
Chem Commun (Camb): 2011, 47(11);3111-3
[PubMed:21264418] [WorldCat.org] [DOI] (I p)

Ellen W Moomaw, Alexander Angerhofer, Patricia Moussatche, Andrew Ozarowski, Inés García-Rubio, Nigel G J Richards
Metal dependence of oxalate decarboxylase activity.
Biochemistry: 2009, 48(26);6116-25
[PubMed:19473032] [WorldCat.org] [DOI] (I p)

Shawn R MacLellan, John D Helmann, Haike Antelmann
The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis.
J Bacteriol: 2009, 191(3);931-9
[PubMed:19047353] [WorldCat.org] [DOI] (I p)

Shawn R MacLellan, Tina Wecke, John D Helmann
A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis.
Mol Microbiol: 2008, 69(4);954-67
[PubMed:18573182] [WorldCat.org] [DOI] (I p)

Haike Antelmann, Stefanie Töwe, Dirk Albrecht, Michael Hecker
The phosphorus source phytate changes the composition of the cell wall proteome in Bacillus subtilis.
J Proteome Res: 2007, 6(2);897-903
[PubMed:17269748] [WorldCat.org] [DOI] (P p)

Clare E M Stevenson, Adam Tanner, Laura Bowater, Stephen Bornemann, David M Lawson
SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source.
Acta Crystallogr D Biol Crystallogr: 2004, 60(Pt 12 Pt 2);2403-6
[PubMed:15583401] [WorldCat.org] [DOI] (P p)

Victoria J Just, Clare E M Stevenson, Laura Bowater, Adam Tanner, David M Lawson, Stephen Bornemann
A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site.
J Biol Chem: 2004, 279(19);19867-74
[PubMed:14871895] [WorldCat.org] [DOI] (P p)

Ruchi Anand, Pieter C Dorrestein, Cynthia Kinsland, Tadhg P Begley, Steven E Ealick
Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution.
Biochemistry: 2002, 41(24);7659-69
[PubMed:12056897] [WorldCat.org] [DOI] (P p)

A Tanner, L Bowater, S A Fairhurst, S Bornemann
Oxalate decarboxylase requires manganese and dioxygen for activity. Overexpression and characterization of Bacillus subtilis YvrK and YoaN.
J Biol Chem: 2001, 276(47);43627-34
[PubMed:11546787] [WorldCat.org] [DOI] (P p)

A Tanner, S Bornemann
Bacillus subtilis YvrK is an acid-induced oxalate decarboxylase.
J Bacteriol: 2000, 182(18);5271-3
[PubMed:10960116] [WorldCat.org] [DOI] (P p)