EzCatDB: D00014
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DB codeD00014
CATH domainDomain 13.10.120.10 : Flavocytochrome B2; Chain A, domain 1
Domain 23.20.20.70 : TIM BarrelCatalytic domain
E.C.1.1.2.3
CSA1fcb
MACiEM0102

CATH domainRelated DB codes (homologues)
3.10.120.10 : Flavocytochrome B2; Chain A, domain 1T00018
3.20.20.70 : TIM BarrelS00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00222,S00847,S00224,S00225,S00226,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
UniProtKBKEGG

P00175
Protein nameCytochrome b2, mitochondrialL-lactate dehydrogenase (cytochrome)
lactic acid dehydrogenase
cytochrome b2 (flavin-free derivative of flavocytochrome b2)
flavocytochrome b2
L-lactate cytochrome c reductase
L(+)-lactate:cytochrome c oxidoreductase
dehydrogenase, lactate (cytochrome)
L-lactate cytochrome c oxidoreductase
lactate dehydrogenase (cytochrome)
lactic cytochrome c reductase
SynonymsEC 1.1.2.3
L-lactate dehydrogenase [Cytochrome]
L-lactate ferricytochrome C oxidoreductase
L-LCR
RefSeqNP_013658.1 (Protein)
NM_001182412.1 (DNA/RNA sequence)
PfamPF00173 (Cyt-b5)
PF01070 (FMN_dh)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism

UniProtKB:Accession NumberP00175
Entry nameCYB2_YEAST
Activity(S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+).
SubunitHomotetramer.
Subcellular locationMitochondrion intermembrane space.
CofactorFMN.,Protoheme IX groups.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00061C00032C00186C00125C00022C00126
CompoundFMNProtoheme(S)-LactateFerricytochrome cPyruvateFerrocytochrome c
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ionaromatic ring (with nitrogen atoms),carboxyl group,heavy metalcarbohydrate,carboxyl groupamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide groupcarbohydrate,carboxyl groupamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group
ChEBI17621
17627
26355
422

32816

PubChem643976

107689

1060

              
1fcbA01UnboundBound:HEMUnboundUnboundUnboundUnbound
1lcoA01UnboundBound:HEMUnboundUnboundUnboundUnbound
1ldcA01UnboundBound:HEMUnboundUnboundUnboundUnbound
1ltdA01UnboundBound:HEMUnboundUnboundUnboundUnbound
1fcbA02Bound:FMNUnboundUnboundUnboundUnboundUnbound
1fcbBBound:FMNUnboundUnboundUnboundAnalogue:PYRUnbound
1lcoA02Bound:FMNUnboundUnboundUnboundAnalogue:PPYUnbound
1lcoBBound:FMNUnboundUnboundUnboundAnalogue:PPYUnbound
1ldcA02Bound:FMNUnboundUnboundUnboundAnalogue:PYRUnbound
1ldcBBound:FMNUnboundUnboundUnboundAnalogue:PYRUnbound
1ltdA02Bound:FMNUnboundUnboundUnboundUnboundUnbound
1ltdBAnalogue:FMN-SO3UnboundUnboundUnboundUnboundUnbound
1qcwA01Analogue:FNSUnboundUnboundUnboundUnboundUnbound
1qcwB01Analogue:FNSUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P00175 & literature [6]
pdbCatalytic residuesCofactor-binding residuescomment
           
1fcbA01 
HIS 43;HIS 66(Fe binding)
 
1lcoA01 
HIS 43;HIS 66(Fe bindind)
 
1ldcA01 
HIS 43;HIS 66(Fe binding)
 
1ltdA01 
HIS 43;HIS 66(Fe binding)
 
1fcbA02TYR 254;ASP 282;HIS 373;ARG 376
 
 
1fcbBTYR 254;ASP 282;HIS 373;ARG 376
 
 
1lcoA02TYR 254;ASP 282;HIS 373;ARG 376
 
mutant Y143F
1lcoBTYR 254;ASP 282;HIS 373;ARG 376
 
mutant Y143F
1ldcA02TYR 254;ASP 282;HIS 373;ARG 376
 
mutant Y143F
1ldcBTYR 254;ASP 282;HIS 373;ARG 376
 
mutant Y143F
1ltdA02TYR 254;ASP 282;HIS 373;ARG 376
 
 
1ltdBTYR 254;ASP 282;HIS 373;ARG 376
 
 
1qcwA01TYR 254;ASP 282;HIS 373;ARG 376
 
mutant R289K;P304F,invisible F304
1qcwB01TYR 254;ASP 282;HIS 373;ARG 376
 
mutant R289K;P304F,invisible F304

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Scheme 3, p.350
[2]p.2632-2833
[3]p.7370
[6]Fig.1, Scheme I, p.6399
[7]Fig.17, p.853, p.856-857
[8]Fig.1, Scheme 1, Scheme 2, p.192
[11]Fig.1, Fig.4, p.805
[12]Fig.1
[14]Fig.2, p.9849
[15]Fig.5, p.626-629
[16]Fig.12
[18]p.6347-6349, Fig.1
[19]Fig.1, p.8593
[26]p.5165-5166
[27]Scheme 23
[28]Fig.1p.4925-4926

references
[1]
PubMed ID6386468
JournalEur J Biochem
Year1984
Volume144
Pages345-51
AuthorsUrban P, Lederer F
TitleBaker's yeast flavocytochrome b2. A mechanistic study of the dehydrohalogenation reaction.
[2]
PubMed ID3554243
JournalProc Natl Acad Sci U S A
Year1987
Volume84
Pages2629-33
AuthorsXia ZX, Shamala N, Bethge PH, Lim LW, Bellamy HD, Xuong NH, Lederer F, Mathews FS
TitleThree-dimensional structure of flavocytochrome b2 from baker's yeast at 3.0-A resolution.
[3]
PubMed ID3061453
JournalBiochemistry
Year1988
Volume27
Pages7365-71
AuthorsUrban P, Chirat I, Lederer F
TitleRat kidney L-2-hydroxyacid oxidase. Structural and mechanistic comparison with flavocytochrome b2 from baker's yeast.
[4]
PubMed ID3058697
JournalJ Biol Chem
Year1988
Volume263
Pages19278-81
AuthorsTegoni M, Mathews FS
TitleCrystallographic study of the complex between sulfite and bakers' yeast flavocytochrome b2.
[5]
PubMed ID2688640
JournalBiochem J
Year1989
Volume263
Pages973-6
AuthorsBlack MT, Gunn FJ, Chapman SK, Reid GA
TitleStructural basis for the kinetic differences between flavocytochromes b2 from the yeasts Hansenula anomala and Saccharomyces cerevisiae.
[6]
PubMed ID2207080
JournalBiochemistry
Year1990
Volume29
Pages6393-400
AuthorsDubois J, Chapman SK, Mathews FS, Reid GA, Lederer F
TitleSubstitution of Tyr254 with Phe at the active site of flavocytochrome b2: consequences on catalysis of lactate dehydrogenation.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID90230315
PubMed ID2329585
JournalJ Mol Biol
Year1990
Volume212
Pages837-63
AuthorsXia ZX, Mathews FS
TitleMolecular structure of flavocytochrome b2 at 2.4 A resolution.
Related PDB1fcb
Related UniProtKBP00175
[8]
PubMed ID1637299
JournalBiochem J
Year1992
Volume285
Pages187-92
AuthorsMiles CS, Rouviere-Fourmy N, Lederer F, Mathews FS, Reid GA, Black MT, Chapman SK
TitleTyr-143 facilitates interdomain electron transfer in flavocytochrome b2.
[9]
PubMed ID8395046
JournalProteins
Year1993
Volume16
Pages408-22
AuthorsTegoni M, White SA, Roussel A, Mathews FS, Cambillau C
TitleA hypothetical complex between crystalline flavocytochrome b2 and cytochrome c.
[10]
PubMed ID7821541
JournalBiochem Soc Trans
Year1994
Volume22
Pages282S
AuthorsDaff S, Manson FD, Reid GA, Chapman SK
TitleManipulation of the substrate specificity of flavocytochrome b2.
[11]
PubMed ID8292608
JournalBiochemistry
Year1994
Volume33
Pages798-806
AuthorsRouviere-Fourmy N, Capeillere-Blandin C, Lederer F
TitleRole of tyrosine 143 in lactate dehydrogenation by flavocytochrome b2. Primary kinetic isotope effect studies with a phenylalanine mutant.
[12]
PubMed ID8142887
JournalProtein Sci
Year1994
Volume3
Pages109-17
AuthorsBalme A, Lederer F
TitleOn the rate of proton exchange with solvent of the catalytic histidine in flavocytochrome b2 (yeast L-lactate dehydrogenase).
[13]
CommentsX-ray crystallography
PubMed ID8003966
JournalProtein Sci
Year1994
Volume3
Pages303-13
AuthorsTegoni M, Cambillau C
TitleThe 2.6-A refined structure of the Escherichia coli recombinant Saccharomyces cerevisiae flavocytochrome b2-sulfite complex.
Related PDB1ltd
[14]
CommentsX-ray crystallography
PubMed ID7632684
JournalBiochemistry
Year1995
Volume34
Pages9840-50
AuthorsTegoni M, Begotti S, Cambillau C
TitleX-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate.
Related PDB1lco,1ldc
[15]
PubMed ID8589072
JournalBiochimie
Year1995
Volume77
Pages621-30
AuthorsGaume B, Sharp RE, Manson FD, Chapman SK, Reid GA, Lederer F
TitleMutation to glutamine of histidine 373, the catalytic base of flavocytochrome b2 (L-lactate dehydrogenase).
[16]
PubMed ID7663348
JournalProtein Sci
Year1995
Volume4
Pages925-35
AuthorsGondry M, Diep Le KH, Manson FD, Chapman SK, Mathews FS, Reid GA, Lederer F
TitleOn the lack of coordination between protein folding and flavin insertion in Escherichia coli for flavocytochrome b2 mutant forms Y254L and D282N.
[17]
PubMed ID8687394
JournalBiochem J
Year1996
Volume316
Pages507-13
AuthorsSharp RE, Chapman SK, Reid GA
TitleModulation of flavocytochrome b2 intraprotein electron transfer via an interdomain hinge region.
[18]
PubMed ID8639579
JournalBiochemistry
Year1996
Volume35
Pages6345-50
AuthorsDaff S, Ingledew WJ, Reid GA, Chapman SK
TitleNew insights into the catalytic cycle of flavocytochrome b2.
[19]
PubMed ID8679620
JournalBiochemistry
Year1996
Volume35
Pages8587-94
AuthorsGondry M, Lederer F
TitleFunctional properties of the histidine-aspartate ion pair of flavocytochrome b2 (L-lactate dehydrogenase): substitution of Asp282 with asparagine.
[20]
PubMed ID8755502
JournalProc Natl Acad Sci U S A
Year1996
Volume93
Pages7496-501
AuthorsMattevi A, Vanoni MA, Todone F, Rizzi M, Teplyakov A, Coda A, Bolognesi M, Curti B
TitleCrystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
[21]
PubMed ID9188712
JournalBiochemistry
Year1997
Volume36
Pages7126-35
AuthorsRouviere N, Mayer M, Tegoni M, Capeillere-Blandin C, Lederer F
TitleMolecular interpretation of inhibition by excess substrate in flavocytochrome b2: a study with wild-type and Y143F mutant enzymes.
[22]
PubMed ID9220981
JournalBiochemistry
Year1997
Volume36
Pages8932-46
AuthorsTegoni M, Gervais M, Desbois A
TitleResonance Raman study on the oxidized and anionic semiquinone forms of flavocytochrome b2 and L-lactate monooxygenase. Influence of the structure and environment of the isoalloxazine ring on the flavin function.
[23]
PubMed ID9639570
JournalBiochem J
Year1998
Volume333
Pages117-20
AuthorsSinclair R, Reid GA, Chapman SK
TitleRe-design of Saccharomyces cerevisiae flavocytochrome b2: introduction of L-mandelate dehydrogenase activity.
[24]
PubMed ID9521665
JournalBiochemistry
Year1998
Volume37
Pages3440-8
AuthorsMiles CS, Lederer F, Le KH
TitleProbing intramolecular electron transfer within flavocytochrome b2 with a monoclonal antibody.
[25]
CommentsX-ray crystallography
PubMed ID10727218
JournalBiochemistry
Year2000
Volume39
Pages3266-75
AuthorsMowat CG, Beaudoin I, Durley RC, Barton JD, Pike AD, Chen ZW, Reid GA, Chapman SK, Mathews FS, Lederer F
TitleKinetic and crystallographic studies on the active site Arg289Lys mutant of flavocytochrome b2 (yeast L-lactate dehydrogenase).
Related PDB1qcw
[26]
PubMed ID10931200
JournalEur J Biochem
Year2000
Volume267
Pages5156-67
AuthorsFleischmann G, Lederer F, Muller F, Bacher A, Ruterjans H
TitleFlavin-protein interactions in flavocytochrome b2 as studied by NMR after reconstitution of the enzyme with 13C- and 15N-labelled flavin.
[27]
PubMed ID11170421
JournalBiochemistry
Year2001
Volume40
Pages994-1001
AuthorsSobrado P, Daubner SC, Fitzpatrick PF
TitleProbing the relative timing of hydrogen abstraction steps in the flavocytochrome b2 reaction with primary and solvent deuterium isotope effects and mutant enzymes.
[28]
PubMed ID11559361
JournalEur J Biochem
Year2001
Volume268
Pages4918-27
AuthorsGondry M, Dubois J, Terrier M, Lederer F
TitleThe catalytic role of tyrosine 254 in flavocytochrome b2 (L-lactate dehydrogenase from baker's yeast). Comparison between the Y254F and Y254L mutant proteins.

comments
This Enzyme (Flavocytochrome b2, E.C. 1.1.2.3) is also called L-lactate dehydrogenase, but different from E.C. 1.1.1.27.
According to the literature [18], this enzyme catalyzes several steps, in which the dehydrogenation of Lactate and electron transfers from b2-heme to cytochrome c occur independently.

createdupdated
2004-07-162009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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