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Cytochrome b2, mitochondrial (EC 1.1.2.3) (L-lactate dehydrogenase [Cytochrome]) (L-lactate ferricytochrome C oxidoreductase) (L-LCR)

 CYB2_YEAST              Reviewed;         591 AA.
P00175; D6VZC0;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
01-APR-1988, sequence version 1.
23-MAY-2018, entry version 195.
RecName: Full=Cytochrome b2, mitochondrial;
EC=1.1.2.3;
AltName: Full=L-lactate dehydrogenase [Cytochrome];
AltName: Full=L-lactate ferricytochrome C oxidoreductase;
Short=L-LCR;
Flags: Precursor;
Name=CYB2; OrderedLocusNames=YML054C; ORFNames=YM9958.08C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3004948;
Guiard B.;
"Structure, expression and regulation of a nuclear gene encoding a
mitochondrial protein: the yeast L(+)-lactate cytochrome c
oxidoreductase (cytochrome b2).";
EMBO J. 4:3265-3272(1985).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169872;
Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S.,
Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A.,
Rice P., Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome
XIII.";
Nature 387:90-93(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
PROTEIN SEQUENCE OF 81-394.
PubMed=6365548; DOI=10.1111/j.1432-1033.1984.tb07976.x;
Ghrir R., Becam A.-M., Lederer F.;
"Primary structure of flavocytochrome b2 from baker's yeast.
Purification by reverse-phase high-pressure liquid chromatography and
sequencing of fragment alpha cyanogen bromide peptides.";
Eur. J. Biochem. 139:59-74(1984).
[5]
PROTEIN SEQUENCE OF 395-591.
PubMed=3902473; DOI=10.1111/j.1432-1033.1985.tb09213.x;
Lederer F., Cortial S., Becam A.-M., Haumont P.-Y., Perez L.;
"Complete amino acid sequence of flavocytochrome b2 from baker's
yeast.";
Eur. J. Biochem. 152:419-428(1985).
[6]
PROTEIN SEQUENCE OF 81-94.
PubMed=165435; DOI=10.1038/255422a0;
Guiard B., Lederer F., Jacq C.;
"More similarity between bakers'yeast L-(+)-lactate dehydrogenase and
liver microsomal sytochrome B5.";
Nature 255:422-423(1975).
[7]
PROTEIN SEQUENCE OF 83-88 AND 564-570, AND SUBCELLULAR LOCATION.
STRAIN=ATCC 201238 / W303-1B;
PubMed=11502169; DOI=10.1021/bi010277r;
Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N.,
Manon S., Schmitter J.-M.;
"Yeast mitochondrial dehydrogenases are associated in a supramolecular
complex.";
Biochemistry 40:9758-9769(2001).
[8]
PROTEIN SEQUENCE OF 88-183.
PubMed=776230; DOI=10.1016/S0300-9084(76)80437-3;
Guiard B., Lederer F.;
"Complete amino acid sequence of the heme-binding core in bakers'
yeast cytochrome b2 (L-(+)-lactate dehydrogenase).";
Biochimie 58:305-316(1976).
[9]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[10]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE
SCALE ANALYSIS].
PubMed=22984289; DOI=10.1074/mcp.M112.021105;
Voegtle F.N., Burkhart J.M., Rao S., Gerbeth C., Hinrichs J.,
Martinou J.C., Chacinska A., Sickmann A., Zahedi R.P., Meisinger C.;
"Intermembrane space proteome of yeast mitochondria.";
Mol. Cell. Proteomics 11:1840-1852(2012).
[11]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
PubMed=2329585; DOI=10.1016/0022-2836(90)90240-M;
Xia Z.-X., Mathews F.S.;
"Molecular structure of flavocytochrome b2 at 2.4-A resolution.";
J. Mol. Biol. 212:837-863(1990).
[12]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 81-591 IN COMPLEXES WITH HEME
AND FMN.
PubMed=11914072; DOI=10.1021/bi0119870;
Cunane L.M., Barton J.D., Chen Z.-W., Welsh F.E., Chapman S.K.,
Reid G.A., Mathews F.S.;
"Crystallographic study of the recombinant flavin-binding domain of
Baker's yeast flavocytochrome b(2): comparison with the intact wild-
type enzyme.";
Biochemistry 41:4264-4272(2002).
-!- CATALYTIC ACTIVITY: (S)-lactate + 2 ferricytochrome c = pyruvate +
2 ferrocytochrome c + 2 H(+).
-!- COFACTOR:
Name=FMN; Xref=ChEBI:CHEBI:58210;
Evidence={ECO:0000269|PubMed:11914072};
-!- COFACTOR:
Name=heme b; Xref=ChEBI:CHEBI:60344;
Evidence={ECO:0000269|PubMed:11914072};
Note=Binds 1 heme b (iron(II)-protoporphyrin IX) group non-
covalently per subunit. {ECO:0000269|PubMed:11914072};
-!- SUBUNIT: Homotetramer.
-!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space
{ECO:0000269|PubMed:11502169, ECO:0000269|PubMed:22984289}.
-!- INDUCTION: By L-lactate. Induced during respiratory adaptation.
-!- MISCELLANEOUS: Present with 4590 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- WEB RESOURCE: Name=Worthington enzyme manual;
URL="http://www.worthington-biochem.com/YLDHS/";
-----------------------------------------------------------------------
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EMBL; X03215; CAA26959.1; -; Genomic_DNA.
EMBL; Z46729; CAA86721.1; -; Genomic_DNA.
EMBL; BK006946; DAA09844.1; -; Genomic_DNA.
PIR; A24583; CBBY2.
RefSeq; NP_013658.1; NM_001182412.1.
PDB; 1FCB; X-ray; 2.40 A; A/B=81-591.
PDB; 1KBI; X-ray; 2.30 A; A/B=81-591.
PDB; 1KBJ; X-ray; 2.50 A; A/B=180-591.
PDB; 1LCO; X-ray; 2.90 A; A/B=81-591.
PDB; 1LDC; X-ray; 2.90 A; A/B=81-591.
PDB; 1LTD; X-ray; 2.60 A; A/B=86-591.
PDB; 1QCW; X-ray; 2.75 A; A/B=182-591.
PDB; 1SZE; X-ray; 3.00 A; A/B=81-591.
PDB; 1SZF; X-ray; 2.70 A; A/B=81-591.
PDB; 1SZG; X-ray; 2.70 A; A/B=81-591.
PDB; 2OZ0; X-ray; 2.80 A; A/B=81-591.
PDB; 3KS0; X-ray; 2.70 A; A/B=86-180.
PDBsum; 1FCB; -.
PDBsum; 1KBI; -.
PDBsum; 1KBJ; -.
PDBsum; 1LCO; -.
PDBsum; 1LDC; -.
PDBsum; 1LTD; -.
PDBsum; 1QCW; -.
PDBsum; 1SZE; -.
PDBsum; 1SZF; -.
PDBsum; 1SZG; -.
PDBsum; 2OZ0; -.
PDBsum; 3KS0; -.
ProteinModelPortal; P00175; -.
SMR; P00175; -.
BioGrid; 35113; 76.
DIP; DIP-5810N; -.
IntAct; P00175; 15.
MINT; P00175; -.
STRING; 4932.YML054C; -.
PaxDb; P00175; -.
PRIDE; P00175; -.
EnsemblFungi; YML054C; YML054C; YML054C.
GeneID; 854950; -.
KEGG; sce:YML054C; -.
EuPathDB; FungiDB:YML054C; -.
SGD; S000004518; CYB2.
GeneTree; ENSGT00390000018717; -.
HOGENOM; HOG000217463; -.
InParanoid; P00175; -.
KO; K00101; -.
OMA; MQLYIYK; -.
OrthoDB; EOG092C43G8; -.
BioCyc; MetaCyc:YML054C-MONOMER; -.
BioCyc; YEAST:YML054C-MONOMER; -.
BRENDA; 1.1.2.3; 984.
Reactome; R-SCE-389661; Glyoxylate metabolism and glycine degradation.
Reactome; R-SCE-390918; Peroxisomal lipid metabolism.
Reactome; R-SCE-9033241; Peroxisomal protein import.
SABIO-RK; P00175; -.
EvolutionaryTrace; P00175; -.
PRO; PR:P00175; -.
Proteomes; UP000002311; Chromosome XIII.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0005743; C:mitochondrial inner membrane; TAS:Reactome.
GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
GO; GO:0005739; C:mitochondrion; IDA:SGD.
GO; GO:0070469; C:respiratory chain; IEA:UniProtKB-KW.
GO; GO:0020037; F:heme binding; IEA:InterPro.
GO; GO:0004460; F:L-lactate dehydrogenase (cytochrome) activity; IDA:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006089; P:lactate metabolic process; IMP:SGD.
CDD; cd02922; FCB2_FMN; 1.
Gene3D; 3.10.120.10; -; 1.
Gene3D; 3.20.20.70; -; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR001199; Cyt_B5-like_heme/steroid-bd.
InterPro; IPR036400; Cyt_B5-like_heme/steroid_sf.
InterPro; IPR018506; Cyt_B5_heme-BS.
InterPro; IPR000262; FMN-dep_DH.
InterPro; IPR037396; FMN_HAD.
InterPro; IPR008259; FMN_hydac_DH_AS.
InterPro; IPR037458; L-MDH/L-LDH_FMN-bd.
Pfam; PF00173; Cyt-b5; 1.
Pfam; PF01070; FMN_dh; 1.
PRINTS; PR00363; CYTOCHROMEB5.
SMART; SM01117; Cyt-b5; 1.
SUPFAM; SSF55856; SSF55856; 1.
PROSITE; PS00191; CYTOCHROME_B5_1; 1.
PROSITE; PS50255; CYTOCHROME_B5_2; 1.
PROSITE; PS00557; FMN_HYDROXY_ACID_DH_1; 1.
PROSITE; PS51349; FMN_HYDROXY_ACID_DH_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing;
Electron transport; Flavoprotein; FMN; Heme; Iron; Metal-binding;
Mitochondrion; Oxidoreductase; Reference proteome; Respiratory chain;
Transit peptide; Transport.
TRANSIT 1 80 Mitochondrion.
{ECO:0000269|PubMed:165435,
ECO:0000269|PubMed:6365548}.
CHAIN 81 591 Cytochrome b2, mitochondrial.
/FTId=PRO_0000006480.
DOMAIN 88 165 Cytochrome b5 heme-binding.
{ECO:0000255|PROSITE-ProRule:PRU00279}.
DOMAIN 197 563 FMN hydroxy acid dehydrogenase.
{ECO:0000255|PROSITE-ProRule:PRU00683}.
REGION 177 190 Hinge.
REGION 567 591 Tail (wraps around the molecular 4-fold
axis).
ACT_SITE 453 453 Proton acceptor.
METAL 123 123 Iron (heme axial ligand).
METAL 146 146 Iron (heme axial ligand).
BINDING 177 177 Heme b.
BINDING 219 219 Heme b.
BINDING 223 223 Heme b.
BINDING 376 376 Heme b.
BINDING 456 456 Substrate.
CONFLICT 165 165 Q -> E (in Ref. 4; AA sequence and 8; AA
sequence). {ECO:0000305}.
CONFLICT 466 466 E -> Q (in Ref. 5; AA sequence).
{ECO:0000305}.
CONFLICT 513 513 R -> E (in Ref. 5; AA sequence).
{ECO:0000305}.
CONFLICT 570 570 V -> P (in Ref. 7; AA sequence).
{ECO:0000305}.
HELIX 95 98 {ECO:0000244|PDB:1KBI}.
STRAND 104 109 {ECO:0000244|PDB:1KBI}.
STRAND 112 115 {ECO:0000244|PDB:1KBI}.
TURN 117 119 {ECO:0000244|PDB:1KBI}.
HELIX 120 122 {ECO:0000244|PDB:1KBI}.
HELIX 127 131 {ECO:0000244|PDB:1KBI}.
TURN 132 135 {ECO:0000244|PDB:1KBI}.
HELIX 139 142 {ECO:0000244|PDB:1KBI}.
HELIX 143 145 {ECO:0000244|PDB:1KBI}.
HELIX 150 154 {ECO:0000244|PDB:1KBI}.
HELIX 157 159 {ECO:0000244|PDB:1KBI}.
STRAND 160 164 {ECO:0000244|PDB:1KBI}.
STRAND 170 173 {ECO:0000244|PDB:1FCB}.
HELIX 183 194 {ECO:0000244|PDB:1KBI}.
HELIX 199 201 {ECO:0000244|PDB:1KBI}.
HELIX 205 215 {ECO:0000244|PDB:1KBI}.
HELIX 218 225 {ECO:0000244|PDB:1KBI}.
STRAND 228 230 {ECO:0000244|PDB:1LDC}.
HELIX 232 239 {ECO:0000244|PDB:1KBI}.
HELIX 240 243 {ECO:0000244|PDB:1KBI}.
STRAND 261 263 {ECO:0000244|PDB:1KBI}.
STRAND 266 274 {ECO:0000244|PDB:1KBI}.
HELIX 280 282 {ECO:0000244|PDB:1KBI}.
TURN 285 288 {ECO:0000244|PDB:1KBI}.
HELIX 289 297 {ECO:0000244|PDB:1KBI}.
STRAND 298 301 {ECO:0000244|PDB:1KBI}.
STRAND 305 307 {ECO:0000244|PDB:1KBI}.
HELIX 315 320 {ECO:0000244|PDB:1KBI}.
STRAND 325 327 {ECO:0000244|PDB:1FCB}.
STRAND 329 333 {ECO:0000244|PDB:1KBI}.
HELIX 339 352 {ECO:0000244|PDB:1KBI}.
STRAND 357 360 {ECO:0000244|PDB:1KBI}.
HELIX 370 377 {ECO:0000244|PDB:1KBI}.
HELIX 398 401 {ECO:0000244|PDB:1KBI}.
STRAND 404 406 {ECO:0000244|PDB:1LTD}.
HELIX 412 421 {ECO:0000244|PDB:1KBI}.
STRAND 426 431 {ECO:0000244|PDB:1KBI}.
HELIX 434 442 {ECO:0000244|PDB:1KBI}.
STRAND 446 450 {ECO:0000244|PDB:1KBI}.
TURN 453 456 {ECO:0000244|PDB:1KBI}.
HELIX 464 476 {ECO:0000244|PDB:1KBI}.
TURN 477 479 {ECO:0000244|PDB:1KBI}.
HELIX 481 483 {ECO:0000244|PDB:1FCB}.
STRAND 484 491 {ECO:0000244|PDB:1KBI}.
HELIX 495 504 {ECO:0000244|PDB:1KBI}.
STRAND 507 511 {ECO:0000244|PDB:1KBI}.
HELIX 513 545 {ECO:0000244|PDB:1KBI}.
HELIX 550 552 {ECO:0000244|PDB:1KBI}.
HELIX 555 557 {ECO:0000244|PDB:1KBI}.
TURN 561 564 {ECO:0000244|PDB:1KBI}.
HELIX 574 579 {ECO:0000244|PDB:1KBI}.
SEQUENCE 591 AA; 65539 MW; DBADA0751B3C5B83 CRC64;
MLKYKPLLKI SKNCEAAILR ASKTRLNTIR AYGSTVPKSK SFEQDSRKRT QSWTALRVGA
ILAATSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN KPDDCWVVIN GYVYDLTRFL
PNHPGGQDVI KFNAGKDVTA IFEPLHAPNV IDKYIAPEKK LGPLQGSMPP ELVCPPYAPG
ETKEDIARKE QLKSLLPPLD NIINLYDFEY LASQTLTKQA WAYYSSGAND EVTHRENHNA
YHRIFFKPKI LVDVRKVDIS TDMLGSHVDV PFYVSATALC KLGNPLEGEK DVARGCGQGV
TKVPQMISTL ASCSPEEIIE AAPSDKQIQW YQLYVNSDRK ITDDLVKNVE KLGVKALFVT
VDAPSLGQRE KDMKLKFSNT KAGPKAMKKT NVEESQGASR ALSKFIDPSL TWKDIEELKK
KTKLPIVIKG VQRTEDVIKA AEIGVSGVVL SNHGGRQLDF SRAPIEVLAE TMPILEQRNL
KDKLEVFVDG GVRRGTDVLK ALCLGAKGVG LGRPFLYANS CYGRNGVEKA IEILRDEIEM
SMRLLGVTSI AELKPDLLDL STLKARTVGV PNDVLYNEVY EGPTLTEFED A


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