NDI1_YEAST
ID NDI1_YEAST Reviewed; 513 AA.
AC P32340; D6W0G4;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 199.
DE RecName: Full=Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial;
DE EC=1.6.5.9;
DE AltName: Full=Internal NADH dehydrogenase;
DE AltName: Full=NADH:ubiquinone reductase (non-electrogenic);
DE Flags: Precursor;
GN Name=NDI1; OrderedLocusNames=YML120C; ORFNames=YM7056.06C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 27-36 AND 41-50.
RC STRAIN=YP102;
RX PubMed=1735444; DOI=10.1111/j.1432-1033.1992.tb16587.x;
RA de Vries S., van Witzenburg R., Grivell L.A., Marres C.A.M.;
RT "Primary structure and import pathway of the rotenone-insensitive NADH-
RT ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae.";
RL Eur. J. Biochem. 203:587-592(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=11502169; DOI=10.1021/bi010277r;
RA Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S.,
RA Schmitter J.-M.;
RT "Yeast mitochondrial dehydrogenases are associated in a supramolecular
RT complex.";
RL Biochemistry 40:9758-9769(2001).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=17761666; DOI=10.1074/mcp.m700098-mcp200;
RA Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B.,
RA van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C.;
RT "Profiling phosphoproteins of yeast mitochondria reveals a role of
RT phosphorylation in assembly of the ATP synthase.";
RL Mol. Cell. Proteomics 6:1896-1906(2007).
CC -!- FUNCTION: Catalyzes the oxidation of NADH generated inside the
CC Mitochondrion.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a quinone + H(+) + NADH = a quinol + NAD(+);
CC Xref=Rhea:RHEA:46160, ChEBI:CHEBI:15378, ChEBI:CHEBI:24646,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:132124; EC=1.6.5.9;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ubiquinone + H(+) + NADH = a ubiquinol + NAD(+);
CC Xref=Rhea:RHEA:23152, Rhea:RHEA-COMP:9565, Rhea:RHEA-COMP:9566,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16389, ChEBI:CHEBI:17976,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC Note=Binds 1 FAD per subunit. {ECO:0000250};
CC -!- INTERACTION:
CC P32340; P32340: NDI1; NbExp=5; IntAct=EBI-11961, EBI-11961;
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:11502169}; Peripheral membrane protein
CC {ECO:0000269|PubMed:11502169}; Matrix side
CC {ECO:0000269|PubMed:11502169}. Note=Bound to the mitochondrial inner
CC membrane facing the matrix site.
CC -!- MISCELLANEOUS: Present with 5240 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NADH dehydrogenase family. {ECO:0000305}.
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DR EMBL; X61590; CAA43787.1; ALT_SEQ; Genomic_DNA.
DR EMBL; Z49218; CAA89160.1; -; Genomic_DNA.
DR EMBL; AY723851; AAU09768.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09778.1; -; Genomic_DNA.
DR PIR; S26704; S26704.
DR RefSeq; NP_013586.1; NM_001182483.1.
DR PDB; 4G6G; X-ray; 2.39 A; A/B=24-513.
DR PDB; 4G6H; X-ray; 2.26 A; A/B=24-513.
DR PDB; 4G73; X-ray; 2.52 A; A/B=24-513.
DR PDB; 4G74; X-ray; 2.48 A; A/B=24-513.
DR PDB; 4G9K; X-ray; 2.70 A; A/B=43-513.
DR PDB; 4GAP; X-ray; 2.90 A; A/B=43-513.
DR PDB; 4GAV; X-ray; 3.00 A; A/B=43-513.
DR PDB; 5YJW; X-ray; 1.85 A; A=30-513.
DR PDB; 5YJX; X-ray; 3.21 A; A/B=28-513.
DR PDBsum; 4G6G; -.
DR PDBsum; 4G6H; -.
DR PDBsum; 4G73; -.
DR PDBsum; 4G74; -.
DR PDBsum; 4G9K; -.
DR PDBsum; 4GAP; -.
DR PDBsum; 4GAV; -.
DR PDBsum; 5YJW; -.
DR PDBsum; 5YJX; -.
DR AlphaFoldDB; P32340; -.
DR SMR; P32340; -.
DR BioGRID; 35084; 78.
DR DIP; DIP-5554N; -.
DR IntAct; P32340; 15.
DR MINT; P32340; -.
DR STRING; 4932.YML120C; -.
DR iPTMnet; P32340; -.
DR UCD-2DPAGE; P32340; -.
DR MaxQB; P32340; -.
DR PaxDb; P32340; -.
DR PRIDE; P32340; -.
DR EnsemblFungi; YML120C_mRNA; YML120C; YML120C.
DR GeneID; 854919; -.
DR KEGG; sce:YML120C; -.
DR SGD; S000004589; NDI1.
DR VEuPathDB; FungiDB:YML120C; -.
DR eggNOG; KOG2495; Eukaryota.
DR HOGENOM; CLU_021377_1_0_1; -.
DR InParanoid; P32340; -.
DR OMA; PYGTLIW; -.
DR BioCyc; MetaCyc:YML120C-MON; -.
DR BioCyc; YEAST:YML120C-MON; -.
DR BRENDA; 1.6.5.9; 984.
DR PRO; PR:P32340; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; P32340; protein.
DR GO; GO:0005743; C:mitochondrial inner membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005759; C:mitochondrial matrix; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008137; F:NADH dehydrogenase (ubiquinone) activity; IDA:SGD.
DR GO; GO:0006120; P:mitochondrial electron transport, NADH to ubiquinone; IDA:SGD.
DR GO; GO:0006116; P:NADH oxidation; IDA:SGD.
DR GO; GO:0043065; P:positive regulation of apoptotic process; IMP:SGD.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR045024; NDH-2.
DR PANTHER; PTHR43706; PTHR43706; 1.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR SUPFAM; SSF51905; SSF51905; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; FAD; Flavoprotein; Membrane;
KW Mitochondrion; Mitochondrion inner membrane; NAD; Oxidoreductase;
KW Reference proteome; Transit peptide; Ubiquinone.
FT TRANSIT 1..26
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:1735444"
FT CHAIN 27..513
FT /note="Rotenone-insensitive NADH-ubiquinone oxidoreductase,
FT mitochondrial"
FT /id="PRO_0000021793"
FT BINDING 55..85
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 229..265
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT VARIANT 10
FT /note="K -> R"
FT STRAND 40..42
FT /evidence="ECO:0007829|PDB:5YJX"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:4G6H"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:4G6G"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 63..71
FT /evidence="ECO:0007829|PDB:5YJW"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 77..84
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 91..96
FT /evidence="ECO:0007829|PDB:5YJW"
FT TURN 97..100
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 104..107
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 111..115
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 122..133
FT /evidence="ECO:0007829|PDB:5YJW"
FT TURN 134..137
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:4G6H"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 170..174
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 178..180
FT /evidence="ECO:0007829|PDB:4G6G"
FT HELIX 188..191
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:4G6G"
FT HELIX 198..215
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 223..228
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 230..234
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 238..253
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 255..258
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 260..265
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 267..271
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 273..277
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 283..295
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 303..309
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 311..319
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:4G74"
FT STRAND 325..331
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 333..337
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:4G6G"
FT HELIX 345..351
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 355..357
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 362..366
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 370..372
FT /evidence="ECO:0007829|PDB:4G6H"
FT STRAND 376..380
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 385..389
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 393..410
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 414..417
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:4G6H"
FT HELIX 429..433
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 445..449
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 455..461
FT /evidence="ECO:0007829|PDB:5YJW"
FT STRAND 464..471
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 472..485
FT /evidence="ECO:0007829|PDB:5YJW"
FT HELIX 489..504
FT /evidence="ECO:0007829|PDB:5YJW"
SQ SEQUENCE 513 AA; 57250 MW; E3A43D75A1ADCF3B CRC64;
MLSKNLYSNK RLLTSTNTLV RFASTRSTGV ENSGAGPTSF KTMKVIDPQH SDKPNVLILG
SGWGAISFLK HIDTKKYNVS IISPRSYFLF TPLLPSAPVG TVDEKSIIEP IVNFALKKKG
NVTYYEAEAT SINPDRNTVT IKSLSAVSQL YQPENHLGLH QAEPAEIKYD YLISAVGAEP
NTFGIPGVTD YGHFLKEIPN SLEIRRTFAA NLEKANLLPK GDPERRRLLS IVVVGGGPTG
VEAAGELQDY VHQDLRKFLP ALAEEVQIHL VEALPIVLNM FEKKLSSYAQ SHLENTSIKV
HLRTAVAKVE EKQLLAKTKH EDGKITEETI PYGTLIWATG NKARPVITDL FKKIPEQNSS
KRGLAVNDFL QVKGSNNIFA IGDNAFAGLP PTAQVAHQEA EYLAKNFDKM AQIPNFQKNL
SSRKDKIDLL FEENNFKPFK YNDLGALAYL GSERAIATIR SGKRTFYTGG GLMTFYLWRI
LYLSMILSAR SRLKVFFDWI KLAFFKRDFF KGL
