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Protein

Cytochrome b2, mitochondrial

Gene

CYB2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Metal bindingi123Iron (heme axial ligand)1
Metal bindingi146Iron (heme axial ligand)1
Binding sitei177Heme b1
Binding sitei219Heme b1
Binding sitei223Heme b1
Binding sitei376Heme b1
Active sitei453Proton acceptor1
Binding sitei456Substrate1

GO - Molecular functioni

GO - Biological processi

  • lactate metabolic process Source: SGD
  • protein targeting to mitochondrion Source: Reactome
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:YML054C-MONOMER.
YEAST:YML054C-MONOMER.
BRENDAi1.1.2.3. 984.
ReactomeiR-SCE-1268020. Mitochondrial protein import.
R-SCE-389661. Glyoxylate metabolism and glycine degradation.
R-SCE-390918. Peroxisomal lipid 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
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YML054C.
SGDiS000004518. CYB2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • mitochondrial inner membrane Source: Reactome
  • mitochondrial intermembrane space Source: SGD
  • mitochondrion Source: SGD
  • respiratory chain Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 80Mitochondrion2 PublicationsAdd BLAST80
ChainiPRO_000000648081 – 591Cytochrome b2, mitochondrialAdd BLAST511

Proteomic databases

PRIDEiP00175.

Expressioni

Inductioni

By L-lactate. Induced during respiratory adaptation.

Interactioni

Subunit structurei

Homotetramer.

Protein-protein interaction databases

BioGridi35113. 28 interactors.
DIPiDIP-5810N.
IntActiP00175. 15 interactors.
MINTiMINT-605329.

Structurei

Secondary structure

1591
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi95 – 98Combined sources4
Beta strandi104 – 109Combined sources6
Beta strandi112 – 115Combined sources4
Turni117 – 119Combined sources3
Helixi120 – 122Combined sources3
Helixi127 – 131Combined sources5
Turni132 – 135Combined sources4
Helixi139 – 142Combined sources4
Helixi143 – 145Combined sources3
Helixi150 – 154Combined sources5
Helixi157 – 159Combined sources3
Beta strandi160 – 164Combined sources5
Beta strandi170 – 173Combined sources4
Helixi183 – 194Combined sources12
Helixi199 – 201Combined sources3
Helixi205 – 215Combined sources11
Helixi218 – 225Combined sources8
Beta strandi228 – 230Combined sources3
Helixi232 – 239Combined sources8
Helixi240 – 243Combined sources4
Beta strandi261 – 263Combined sources3
Beta strandi266 – 274Combined sources9
Helixi280 – 282Combined sources3
Turni285 – 288Combined sources4
Helixi289 – 297Combined sources9
Beta strandi298 – 301Combined sources4
Beta strandi305 – 307Combined sources3
Helixi315 – 320Combined sources6
Beta strandi325 – 327Combined sources3
Beta strandi329 – 333Combined sources5
Helixi339 – 352Combined sources14
Beta strandi357 – 360Combined sources4
Helixi370 – 377Combined sources8
Helixi398 – 401Combined sources4
Beta strandi404 – 406Combined sources3
Helixi412 – 421Combined sources10
Beta strandi426 – 431Combined sources6
Helixi434 – 442Combined sources9
Beta strandi446 – 450Combined sources5
Turni453 – 456Combined sources4
Helixi464 – 476Combined sources13
Turni477 – 479Combined sources3
Helixi481 – 483Combined sources3
Beta strandi484 – 491Combined sources8
Helixi495 – 504Combined sources10
Beta strandi507 – 511Combined sources5
Helixi513 – 545Combined sources33
Helixi550 – 552Combined sources3
Helixi555 – 557Combined sources3
Turni561 – 564Combined sources4
Helixi574 – 579Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00175.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini88 – 165Cytochrome b5 heme-bindingPROSITE-ProRule annotationAdd BLAST78
Domaini197 – 563FMN hydroxy acid dehydrogenasePROSITE-ProRule annotationAdd BLAST367

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni177 – 190HingeAdd BLAST14
Regioni567 – 591Tail (wraps around the molecular 4-fold axis)Add BLAST25

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

GeneTreeiENSGT00390000018717.
HOGENOMiHOG000217463.
InParanoidiP00175.
KOiK00101.
OMAiKVIREMW.
OrthoDBiEOG092C43G8.

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.
SMARTiSM01117. Cyt-b5. 1 hit.
[Graphical view]
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)DescriptionActionsGraphical viewLength
Sequence conflicti165Q → E AA sequence (PubMed:6365548).Curated1
Sequence conflicti165Q → E AA sequence (PubMed:776230).Curated1
Sequence conflicti466E → Q AA sequence (PubMed:3902473).Curated1
Sequence conflicti513R → E AA sequence (PubMed:3902473).Curated1
Sequence conflicti570V → P AA sequence (PubMed:11502169).Curated1

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.
PIRiA24583. CBBY2.
RefSeqiNP_013658.1. NM_001182412.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35113. 28 interactors.
DIPiDIP-5810N.
IntActiP00175. 15 interactors.
MINTiMINT-605329.

Proteomic databases

PRIDEiP00175.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YML054C.
SGDiS000004518. CYB2.

Phylogenomic databases

GeneTreeiENSGT00390000018717.
HOGENOMiHOG000217463.
InParanoidiP00175.
KOiK00101.
OMAiKVIREMW.
OrthoDBiEOG092C43G8.

Enzyme and pathway databases

BioCyciMetaCyc:YML054C-MONOMER.
YEAST:YML054C-MONOMER.
BRENDAi1.1.2.3. 984.
ReactomeiR-SCE-1268020. Mitochondrial protein import.
R-SCE-389661. Glyoxylate metabolism and glycine degradation.
R-SCE-390918. Peroxisomal lipid metabolism.
SABIO-RKP00175.

Miscellaneous databases

EvolutionaryTraceiP00175.
PROiP00175.

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.
SMARTiSM01117. Cyt-b5. 1 hit.
[Graphical view]
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]
ProtoNetiSearch...

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 2, 2016
This is version 183 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.