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P00175

- CYB2_YEAST

UniProt

P00175 - CYB2_YEAST

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Protein

Cytochrome b2, mitochondrial

Gene

CYB2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

(S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H+.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi123 – 1231Iron (heme axial ligand)
Metal bindingi146 – 1461Iron (heme axial ligand)
Binding sitei177 – 1771Heme b
Binding sitei219 – 2191Heme b
Binding sitei223 – 2231Heme b
Binding sitei376 – 3761Heme b
Active sitei453 – 4531Proton acceptor
Binding sitei456 – 4561Substrate

GO - Molecular functioni

  1. FMN binding Source: InterPro
  2. heme binding Source: InterPro
  3. L-lactate dehydrogenase (cytochrome) activity Source: SGD
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. lactate metabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Respiratory chain, Transport

Keywords - Ligandi

Flavoprotein, FMN, Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-12911.
YEAST:YML054C-MONOMER.
ReactomeiREACT_189012. Mitochondrial protein import.
REACT_246681. Glyoxylate metabolism.
SABIO-RKP00175.

Names & Taxonomyi

Protein namesi
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 namesi
Name:CYB2
Ordered Locus Names:YML054C
ORF Names:YM9958.08C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIII

Organism-specific databases

CYGDiYML054c.
SGDiS000004518. CYB2.

Subcellular locationi

Mitochondrion intermembrane space 1 Publication

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. mitochondrial inner membrane Source: Reactome
  3. mitochondrial intermembrane space Source: SGD
  4. mitochondrion Source: SGD
  5. respiratory chain Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 8080Mitochondrion2 PublicationsAdd
BLAST
Chaini81 – 591511Cytochrome b2, mitochondrialPRO_0000006480Add
BLAST

Proteomic databases

PaxDbiP00175.
PeptideAtlasiP00175.

Expressioni

Inductioni

By L-lactate. Induced during respiratory adaptation.

Gene expression databases

GenevestigatoriP00175.

Interactioni

Subunit structurei

Homotetramer.

Protein-protein interaction databases

BioGridi35113. 28 interactions.
DIPiDIP-5810N.
IntActiP00175. 9 interactions.
MINTiMINT-605329.
STRINGi4932.YML054C.

Structurei

Secondary structure

1
591
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi95 – 984Combined sources
Beta strandi104 – 1096Combined sources
Beta strandi112 – 1154Combined sources
Turni117 – 1193Combined sources
Helixi120 – 1223Combined sources
Helixi127 – 1315Combined sources
Turni132 – 1354Combined sources
Helixi139 – 1424Combined sources
Helixi143 – 1453Combined sources
Helixi150 – 1545Combined sources
Helixi157 – 1593Combined sources
Beta strandi160 – 1645Combined sources
Beta strandi170 – 1734Combined sources
Helixi183 – 19412Combined sources
Helixi199 – 2013Combined sources
Helixi205 – 21511Combined sources
Helixi218 – 2258Combined sources
Beta strandi228 – 2303Combined sources
Helixi232 – 2398Combined sources
Helixi240 – 2434Combined sources
Beta strandi261 – 2633Combined sources
Beta strandi266 – 2749Combined sources
Helixi280 – 2823Combined sources
Turni285 – 2884Combined sources
Helixi289 – 2979Combined sources
Beta strandi298 – 3014Combined sources
Beta strandi305 – 3073Combined sources
Helixi315 – 3206Combined sources
Beta strandi325 – 3273Combined sources
Beta strandi329 – 3335Combined sources
Helixi339 – 35214Combined sources
Beta strandi357 – 3604Combined sources
Helixi370 – 3778Combined sources
Helixi398 – 4014Combined sources
Beta strandi404 – 4063Combined sources
Helixi412 – 42110Combined sources
Beta strandi426 – 4316Combined sources
Helixi434 – 4429Combined sources
Beta strandi446 – 4505Combined sources
Turni453 – 4564Combined sources
Helixi464 – 47613Combined sources
Turni477 – 4793Combined sources
Helixi481 – 4833Combined sources
Beta strandi484 – 4918Combined sources
Helixi495 – 50410Combined sources
Beta strandi507 – 5115Combined sources
Helixi513 – 54533Combined sources
Helixi550 – 5523Combined sources
Helixi555 – 5573Combined sources
Turni561 – 5644Combined sources
Helixi574 – 5796Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FCBX-ray2.40A/B81-591[»]
1KBIX-ray2.30A/B81-591[»]
1KBJX-ray2.50A/B180-591[»]
1LCOX-ray2.90A/B81-591[»]
1LDCX-ray2.90A/B81-591[»]
1LTDX-ray2.60A/B86-591[»]
1QCWX-ray2.75A/B182-591[»]
1SZEX-ray3.00A/B81-591[»]
1SZFX-ray2.70A/B81-591[»]
1SZGX-ray2.70A/B81-591[»]
2OZ0X-ray2.80A/B81-591[»]
3KS0X-ray2.70A/B86-180[»]
ProteinModelPortaliP00175.
SMRiP00175. Positions 81-591.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00175.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini88 – 16578Cytochrome b5 heme-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini197 – 563367FMN hydroxy acid dehydrogenasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni177 – 19014HingeAdd
BLAST
Regioni567 – 59125Tail (wraps around the molecular 4-fold axis)Add
BLAST

Sequence similaritiesi

Contains 1 cytochrome b5 heme-binding domain.PROSITE-ProRule annotation
Contains 1 FMN hydroxy acid dehydrogenase domain.PROSITE-ProRule annotation

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG1304.
GeneTreeiENSGT00390000018717.
HOGENOMiHOG000217463.
InParanoidiP00175.
KOiK00101.
OMAiAWFQSIT.
OrthoDBiEOG7N63X3.

Family and domain databases

Gene3Di3.10.120.10. 1 hit.
3.20.20.70. 1 hit.
InterProiIPR013785. 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]
PfamiPF00173. Cyt-b5. 1 hit.
PF01070. FMN_dh. 1 hit.
[Graphical view]
PRINTSiPR00363. CYTOCHROMEB5.
SUPFAMiSSF55856. SSF55856. 1 hit.
PROSITEiPS00191. 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]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00175-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLKYKPLLKI SKNCEAAILR ASKTRLNTIR AYGSTVPKSK SFEQDSRKRT
60 70 80 90 100
QSWTALRVGA ILAATSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN
110 120 130 140 150
KPDDCWVVIN GYVYDLTRFL PNHPGGQDVI KFNAGKDVTA IFEPLHAPNV
160 170 180 190 200
IDKYIAPEKK LGPLQGSMPP ELVCPPYAPG ETKEDIARKE QLKSLLPPLD
210 220 230 240 250
NIINLYDFEY LASQTLTKQA WAYYSSGAND EVTHRENHNA YHRIFFKPKI
260 270 280 290 300
LVDVRKVDIS TDMLGSHVDV PFYVSATALC KLGNPLEGEK DVARGCGQGV
310 320 330 340 350
TKVPQMISTL ASCSPEEIIE AAPSDKQIQW YQLYVNSDRK ITDDLVKNVE
360 370 380 390 400
KLGVKALFVT VDAPSLGQRE KDMKLKFSNT KAGPKAMKKT NVEESQGASR
410 420 430 440 450
ALSKFIDPSL TWKDIEELKK KTKLPIVIKG VQRTEDVIKA AEIGVSGVVL
460 470 480 490 500
SNHGGRQLDF SRAPIEVLAE TMPILEQRNL KDKLEVFVDG GVRRGTDVLK
510 520 530 540 550
ALCLGAKGVG LGRPFLYANS CYGRNGVEKA IEILRDEIEM SMRLLGVTSI
560 570 580 590
AELKPDLLDL STLKARTVGV PNDVLYNEVY EGPTLTEFED A
Length:591
Mass (Da):65,539
Last modified:April 1, 1988 - v1
Checksum:iDBADA0751B3C5B83
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti165 – 1651Q → E AA sequence (PubMed:6365548)Curated
Sequence conflicti165 – 1651Q → E AA sequence (PubMed:776230)Curated
Sequence conflicti466 – 4661E → Q AA sequence (PubMed:3902473)Curated
Sequence conflicti513 – 5131R → E AA sequence (PubMed:3902473)Curated
Sequence conflicti570 – 5701V → P AA sequence (PubMed:11502169)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03215 Genomic DNA. Translation: CAA26959.1.
Z46729 Genomic DNA. Translation: CAA86721.1.
BK006946 Genomic DNA. Translation: DAA09844.1.
PIRiA24583. CBBY2.
RefSeqiNP_013658.1. NM_001182412.1.

Genome annotation databases

EnsemblFungiiYML054C; YML054C; YML054C.
GeneIDi854950.
KEGGisce:YML054C.

Cross-referencesi

Web resourcesi

Worthington enzyme manual

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03215 Genomic DNA. Translation: CAA26959.1 .
Z46729 Genomic DNA. Translation: CAA86721.1 .
BK006946 Genomic DNA. Translation: DAA09844.1 .
PIRi A24583. CBBY2.
RefSeqi NP_013658.1. NM_001182412.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
ProteinModelPortali P00175.
SMRi P00175. Positions 81-591.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35113. 28 interactions.
DIPi DIP-5810N.
IntActi P00175. 9 interactions.
MINTi MINT-605329.
STRINGi 4932.YML054C.

Proteomic databases

PaxDbi P00175.
PeptideAtlasi P00175.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YML054C ; YML054C ; YML054C .
GeneIDi 854950.
KEGGi sce:YML054C.

Organism-specific databases

CYGDi YML054c.
SGDi S000004518. CYB2.

Phylogenomic databases

eggNOGi COG1304.
GeneTreei ENSGT00390000018717.
HOGENOMi HOG000217463.
InParanoidi P00175.
KOi K00101.
OMAi AWFQSIT.
OrthoDBi EOG7N63X3.

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-12911.
YEAST:YML054C-MONOMER.
Reactomei REACT_189012. Mitochondrial protein import.
REACT_246681. Glyoxylate metabolism.
SABIO-RK P00175.

Miscellaneous databases

EvolutionaryTracei P00175.
NextBioi 978016.

Gene expression databases

Genevestigatori P00175.

Family and domain databases

Gene3Di 3.10.120.10. 1 hit.
3.20.20.70. 1 hit.
InterProi 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 ]
Pfami PF00173. Cyt-b5. 1 hit.
PF01070. FMN_dh. 1 hit.
[Graphical view ]
PRINTSi PR00363. CYTOCHROMEB5.
SUPFAMi SSF55856. SSF55856. 1 hit.
PROSITEi 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 ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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. 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 81-591 IN COMPLEXES WITH HEME AND FMN.

Entry informationi

Entry nameiCYB2_YEAST
AccessioniPrimary (citable) accession number: P00175
Secondary accession number(s): D6VZC0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: April 1, 1988
Last modified: November 26, 2014
This is version 164 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4590 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3