Reviewed, UniProtKB/Swiss-Prot P00175 (CYB2_YEAST)

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 (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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.6
Induction	By L-lactate. Induced during respiratory adaptation.
Miscellaneous	Present with 4590 molecules/cell in log phase SD medium. Ref.8
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
Gene Ontology (GO)
Biological process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW lactate metabolic process Inferred from mutant phenotype. Source: SGD transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	mitochondrial intermembrane space Ref.1 Inferred from direct assay. Source: SGD respiratory chain Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	L-lactate dehydrogenase (cytochrome) activity Ref.1 Inferred from direct assay. Source: SGD electron carrier activity Inferred from electronic annotation. Source: InterPro heme binding Inferred from electronic annotation. Source: InterPro
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.3 Ref.5

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 Ref.3

Sequence conflict

165

1

Q → E Ref.7

Sequence conflict

466

1

E → Q AA sequence Ref.4

Sequence conflict

513

1

R → E AA sequence Ref.4

Sequence conflict

570

1

V → P AA sequence Ref.6

Secondary structure

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591

Helix Strand Turn

Details...

Turn

93 – 98

6

Helix

102 – 104

3

Beta strand

106 – 109

4

Beta strand

112 – 115

4

Turn

117 – 119

3

Helix

120 – 122

3

Helix

128 – 131

4

Beta strand

135 – 137

3

Helix

139 – 142

4

Helix

143 – 145

3

Helix

150 – 154

5

Helix

157 – 159

3

Beta strand

160 – 166

7

Beta strand

170 – 173

4

Helix

185 – 191

7

Beta strand

192 – 194

3

Helix

199 – 201

3

Helix

206 – 215

10

Helix

218 – 225

8

Helix

232 – 239

8

Helix

240 – 243

4

Beta strand

261 – 263

3

Beta strand

266 – 274

9

Turn

280 – 283

4

Turn

285 – 288

4

Helix

289 – 297

9

Beta strand

298 – 301

4

Beta strand

305 – 308

4

Helix

315 – 320

6

Beta strand

325 – 327

3

Beta strand

329 – 333

5

Helix

339 – 351

13

Beta strand

357 – 360

4

Helix

370 – 376

7

Helix

412 – 420

9

Beta strand

426 – 431

6

Helix

434 – 442

9

Beta strand

446 – 450

5

Turn

453 – 456

4

Helix

464 – 477

14

Helix

481 – 483

3

Beta strand

484 – 491

8

Helix

495 – 503

9

Beta strand

507 – 512

6

Helix

513 – 545

33

Helix

550 – 552

3

Helix

555 – 557

3

Turn

561 – 564

4

Beta strand

566 – 569

4

Helix

574 – 579

6

Sequences

	Sequence		Length	Mass (Da)
	P00175-1 [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: 3004948] [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: 9169872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"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: 6365548] [Abstract] Cited for: PROTEIN SEQUENCE OF 81-394.
[4]	"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: 3902473] [Abstract] Cited for: PROTEIN SEQUENCE OF 395-591.
[5]	"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: 165435] [Abstract] Cited for: PROTEIN SEQUENCE OF 81-94.
[6]	"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: 11502169] [Abstract] Cited for: PROTEIN SEQUENCE OF 83-88 AND 564-570, SUBCELLULAR LOCATION. Strain: ATCC 201238 / W303-1B.
[7]	"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: 776230] [Abstract] Cited for: PROTEIN SEQUENCE OF 88-183.
[8]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"Molecular structure of flavocytochrome b2 at 2.4-A resolution." Xia Z.-X., Mathews F.S. J. Mol. Biol. 212:837-863(1990) [PubMed: 2329585] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
[10]	"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: 11914072] [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

EMBLGenBankDDBJ

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

PIR

CBBY2. A24583.

RefSeq

NP_013658.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5810N.

IntAct

P00175. 1 interaction.

STRING

P00175.

Proteomic databases

PeptideAtlas

P00175.

Genome annotation databases

Ensembl

YML054C; YML054C; YML054C; Saccharomyces cerevisiae. [Genome view]

GeneID

854950.

GenomeReviews

Gene locus YML054C in contig Z71257_GR.

KEGG

sce:YML054C.

NMPDR

fig|4932.3.peg.4696.

Organism-specific databases

CYGD

YML054c.

SGD

S000004518. CYB2.

Phylogenomic databases

HOGENOM

P00175.

OMA

QWLQLYV.

Enzyme and pathway databases

BioCyc

MetaCyc:MON-12911.

BRENDA

1.1.2.3. 250.

Gene expression databases

ArrayExpress

P00175.

Genevestigator

P00175.

GermOnline

YML054C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR013785. Aldolase_TIM.
IPR001199. Cyt_B5.
IPR018506. Cyt_B5_heme-BS.
IPR000262. FMN-dep_DH.
IPR017934. FMN-dep_OHA_DH.
IPR008259. FMN_hydac_DH_AS.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.
G3DSA:3.10.120.10. Cyt_B5. 1 hit.

Pfam

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

PRINTS

PR00363. CYTOCHROMEB5.

ProDom

PD000612. Cyt_B5. 1 hit.
[Graphical view] [Entries sharing at least one domain]

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 Resources

NextBio

978016.

Entry information

Entry name

CYB2_YEAST

Accession

Primary (citable) accession number: P00175

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	April 1, 1988
Last modified:	November 3, 2009
This is version 122 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)