P00175 (CYB2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cytochrome b2, mitochondrial
EC=1.1.2.3

Alternative name(s):
L-lactate dehydrogenase [Cytochrome]
L-lactate ferricytochrome C oxidoreductase
Short name=L-LCR

Gene names

Name:	CYB2
Ordered Locus Names:	YML054C
ORF Names:	YM9958.08C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	591 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	(S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H+.
Cofactor	FMN. Protoheme IX groups.
Subunit structure	Homotetramer.
Subcellular location	Mitochondrion intermembrane space Ref.7.
Induction	By L-lactate. Induced during respiratory adaptation.
Miscellaneous	Present with 4590 molecules/cell in log phase SD medium.
Sequence similarities	Contains 1 cytochrome b5 heme-binding domain. Contains 1 FMN hydroxy acid dehydrogenase domain.

Ontologies

Keywords
Biological process	Electron transport Respiratory chain Transport
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	FMN Flavoprotein Heme Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW lactate metabolic process Inferred from mutant phenotype PubMed 8492799. Source: SGD
Cellular_component	cytosol Traceable author statement. Source: Reactome mitochondrial inner membrane Traceable author statement. Source: Reactome mitochondrial intermembrane space Inferred from direct assay Ref.1PubMed 6290489. Source: SGD respiratory chain Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	FMN binding Inferred from electronic annotation. Source: InterPro L-lactate dehydrogenase (cytochrome) activity Inferred from direct assay Ref.1. Source: SGD heme binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 80

80

Mitochondrion Ref.4 Ref.6

Chain

81 – 591

511

Cytochrome b2, mitochondrial

PRO_0000006480

Regions

Domain

88 – 165

78

Cytochrome b5 heme-binding

Domain

197 – 563

367

FMN hydroxy acid dehydrogenase

Region

177 – 190

14

Hinge

Region

567 – 591

25

Tail (wraps around the molecular 4-fold axis)

Sites

Active site

453

1

Proton acceptor

Metal binding

123

1

Iron (heme axial ligand) By similarity

Metal binding

146

1

Iron (heme axial ligand) By similarity

Binding site

456

1

Substrate

Experimental info

Sequence conflict

165

1

Q → E AA sequence Ref.4

Sequence conflict

165

1

Q → E AA sequence Ref.8

Sequence conflict

466

1

E → Q AA sequence Ref.5

Sequence conflict

513

1

R → E AA sequence Ref.5

Sequence conflict

570

1

V → P AA sequence Ref.7

Secondary structure

1

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591

Helix Strand Turn

Details...

Helix

95 – 98

4

Beta strand

104 – 109

6

Beta strand

112 – 115

4

Turn

117 – 119

3

Helix

120 – 122

3

Helix

127 – 131

5

Turn

132 – 135

4

Helix

139 – 142

4

Helix

143 – 145

3

Helix

150 – 154

5

Helix

157 – 159

3

Beta strand

160 – 164

5

Beta strand

170 – 173

4

Helix

183 – 194

12

Helix

199 – 201

3

Helix

205 – 215

11

Helix

218 – 225

8

Beta strand

228 – 230

3

Helix

232 – 239

8

Helix

240 – 243

4

Beta strand

261 – 263

3

Beta strand

266 – 274

9

Helix

280 – 282

3

Turn

285 – 288

4

Helix

289 – 297

9

Beta strand

298 – 301

4

Beta strand

305 – 307

3

Helix

315 – 320

6

Beta strand

325 – 327

3

Beta strand

329 – 333

5

Helix

339 – 352

14

Beta strand

357 – 360

4

Helix

370 – 377

8

Helix

398 – 401

4

Beta strand

404 – 406

3

Helix

412 – 421

10

Beta strand

426 – 431

6

Helix

434 – 442

9

Beta strand

446 – 450

5

Turn

453 – 456

4

Helix

464 – 476

13

Turn

477 – 479

3

Helix

481 – 483

3

Beta strand

484 – 491

8

Helix

495 – 504

10

Beta strand

507 – 511

5

Helix

513 – 545

33

Helix

550 – 552

3

Helix

555 – 557

3

Turn

561 – 564

4

Helix

574 – 579

6

Sequences

	Sequence		Length	Mass (Da)
	P00175 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: DBADA0751B3C5B83	FASTA	591	65,539
	10 20 30 40 50 60 MLKYKPLLKI SKNCEAAILR ASKTRLNTIR AYGSTVPKSK SFEQDSRKRT QSWTALRVGA 70 80 90 100 110 120 ILAATSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN KPDDCWVVIN GYVYDLTRFL 130 140 150 160 170 180 PNHPGGQDVI KFNAGKDVTA IFEPLHAPNV IDKYIAPEKK LGPLQGSMPP ELVCPPYAPG 190 200 210 220 230 240 ETKEDIARKE QLKSLLPPLD NIINLYDFEY LASQTLTKQA WAYYSSGAND EVTHRENHNA 250 260 270 280 290 300 YHRIFFKPKI LVDVRKVDIS TDMLGSHVDV PFYVSATALC KLGNPLEGEK DVARGCGQGV 310 320 330 340 350 360 TKVPQMISTL ASCSPEEIIE AAPSDKQIQW YQLYVNSDRK ITDDLVKNVE KLGVKALFVT 370 380 390 400 410 420 VDAPSLGQRE KDMKLKFSNT KAGPKAMKKT NVEESQGASR ALSKFIDPSL TWKDIEELKK 430 440 450 460 470 480 KTKLPIVIKG VQRTEDVIKA AEIGVSGVVL SNHGGRQLDF SRAPIEVLAE TMPILEQRNL 490 500 510 520 530 540 KDKLEVFVDG GVRRGTDVLK ALCLGAKGVG LGRPFLYANS CYGRNGVEKA IEILRDEIEM 550 560 570 580 590 SMRLLGVTSI AELKPDLLDL STLKARTVGV PNDVLYNEVY EGPTLTEFED A

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure, expression and regulation of a nuclear gene encoding a mitochondrial protein: the yeast L(+)-lactate cytochrome c oxidoreductase (cytochrome b2)." Guiard B. EMBO J. 4:3265-3272(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." 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. Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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." Ghrir R., Becam A.-M., Lederer F. Eur. J. Biochem. 139:59-74(1984) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 81-394.
[5]	"Complete amino acid sequence of flavocytochrome b2 from baker's yeast." Lederer F., Cortial S., Becam A.-M., Haumont P.-Y., Perez L. Eur. J. Biochem. 152:419-428(1985) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 395-591.
[6]	"More similarity between bakers'yeast L-(+)-lactate dehydrogenase and liver microsomal sytochrome B5." Guiard B., Lederer F., Jacq C. Nature 255:422-423(1975) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 81-94.
[7]	"Yeast mitochondrial dehydrogenases are associated in a supramolecular complex." Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M. Biochemistry 40:9758-9769(2001) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 83-88 AND 564-570, SUBCELLULAR LOCATION. Strain: ATCC 201238 / W303-1B.
[8]	"Complete amino acid sequence of the heme-binding core in bakers' yeast cytochrome b2 (L-(+)-lactate dehydrogenase)." Guiard B., Lederer F. Biochimie 58:305-316(1976) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 88-183.
[9]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Molecular structure of flavocytochrome b2 at 2.4-A resolution." Xia Z.-X., Mathews F.S. J. Mol. Biol. 212:837-863(1990) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
[11]	"Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme." Cunane L.M., Barton J.D., Chen Z.-W., Welsh F.E., Chapman S.K., Reid G.A., Mathews F.S. Biochemistry 41:4264-4272(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 180-591.
+	Additional computationally mapped references.

Web resources

Worthington enzyme manual

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X03215 Genomic DNA. Translation: CAA26959.1.
Z46729 Genomic DNA. Translation: CAA86721.1.
BK006946 Genomic DNA. Translation: DAA09844.1.

PIR

CBBY2. A24583.

RefSeq

NP_013658.1. NM_001182412.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FCB	X-ray	2.40	A/B	81-591	[»]
1KBI	X-ray	2.30	A/B	81-591	[»]
1KBJ	X-ray	2.50	A/B	180-591	[»]
1LCO	X-ray	2.90	A/B	81-591	[»]
1LDC	X-ray	2.90	A/B	81-591	[»]
1LTD	X-ray	2.60	A/B	86-591	[»]
1QCW	X-ray	2.75	A/B	182-591	[»]
1SZE	X-ray	3.00	A/B	81-591	[»]
1SZF	X-ray	2.70	A/B	81-591	[»]
1SZG	X-ray	2.70	A/B	81-591	[»]
2OZ0	X-ray	2.80	A/B	81-591	[»]
3KS0	X-ray	2.70	A/B	86-180	[»]

ProteinModelPortal

P00175.

SMR

P00175. Positions 81-591.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5810N.

IntAct

P00175. 1 interaction.

MINT

MINT-605329.

STRING

4932.YML054C.

Proteomic databases

PaxDb

P00175.

PeptideAtlas

P00175.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YML054C; YML054C; YML054C.

GeneID

854950.

KEGG

sce:YML054C.

Organism-specific databases

CYGD

YML054c.

SGD

S000004518. CYB2.

Phylogenomic databases

eggNOG

COG1304.

GeneTree

ENSGT00390000018717.

HOGENOM

HOG000217463.

KO

K00101.

OMA

AYHRIFF.

OrthoDB

EOG4NZZ2Q.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-12911.

Reactome

REACT_118590. Mitochondrial Protein Import (yeast).
REACT_85873. Metabolism of proteins.

SABIO-RK

P00175.

Gene expression databases

Genevestigator

P00175.

GermOnline

YML054C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.10.120.10. 1 hit.
3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR012133. Alpha-hydoxy_acid_DH_FMN.
IPR001199. Cyt_B5-like_heme/steroid-bd.
IPR018506. Cyt_B5_heme-BS.
IPR000262. FMN-dep_DH.
IPR008259. FMN_hydac_DH_AS.
[Graphical view]

Pfam

PF00173. Cyt-b5. 1 hit.
PF01070. FMN_dh. 1 hit.
[Graphical view]

PRINTS

PR00363. CYTOCHROMEB5.

SUPFAM

SSF55856. Cyt_B5. 1 hit.

PROSITE

PS00191. CYTOCHROME_B5_1. 1 hit.
PS50255. CYTOCHROME_B5_2. 1 hit.
PS00557. FMN_HYDROXY_ACID_DH_1. 1 hit.
PS51349. FMN_HYDROXY_ACID_DH_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00175.

NextBio

978016.

Entry information

Entry name

CYB2_YEAST

Accession

Primary (citable) accession number: P00175
Secondary accession number(s): D6VZC0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	April 1, 1988
Last modified:	April 3, 2013
This is version 150 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program