CYS3_YEAST
ID CYS3_YEAST Reviewed; 394 AA.
AC P31373; D6VPK6;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=Cystathionine gamma-lyase;
DE Short=gamma-CTLase {ECO:0000303|PubMed:1577698};
DE EC=4.4.1.1 {ECO:0000269|PubMed:1577698, ECO:0000269|PubMed:8335636, ECO:0000269|PubMed:8511969};
DE AltName: Full=Gamma-cystathionase;
DE AltName: Full=Sulfur transfer protein 1;
GN Name=CYS3 {ECO:0000303|PubMed:1577698};
GN Synonyms=CYI1 {ECO:0000303|PubMed:1577698}, STR1;
GN OrderedLocusNames=YAL012W; ORFNames=FUN35;
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], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=1577698; DOI=10.1128/jb.174.10.3339-3347.1992;
RA Ono B., Tanaka K., Naito K., Heike C., Shinoda S., Yamamoto S., Ohmori S.,
RA Oshima T., Toh-e A.;
RT "Cloning and characterization of the CYS3 (CYI1) gene of Saccharomyces
RT cerevisiae.";
RL J. Bacteriol. 174:3339-3347(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBUNIT.
RC STRAIN=DBY939;
RX PubMed=8335636; DOI=10.1128/jb.175.15.4800-4808.1993;
RA Yamagata S., D'Andrea R.J., Fujisaki S., Isaji M., Nakamura K.;
RT "Cloning and bacterial expression of the CYS3 gene encoding cystathionine
RT gamma-lyase of Saccharomyces cerevisiae and the physicochemical and
RT enzymatic properties of the protein.";
RL J. Bacteriol. 175:4800-4808(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=8511966; DOI=10.1002/yea.320090406;
RA Barton A.B., Kaback D.B., Clark M.W., Keng T., Ouellette B.F.F.,
RA Storms R.K., Zeng B., Zhong W.W., Fortin N., Delaney S., Bussey H.;
RT "Physical localization of yeast CYS3, a gene whose product resembles the
RT rat gamma-cystathionase and Escherichia coli cystathionine gamma-synthase
RT enzymes.";
RL Yeast 9:363-369(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=8458570; DOI=10.1139/g93-005;
RA Ouellette B.F.F., Clark M.W., Keng T., Storms R.K., Zhong W.-W., Zeng B.,
RA Fortin N., Delaney S., Barton A.B., Kaback D.B., Bussey H.;
RT "Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32
RT kb region between the LTE1 and SPO7 genes.";
RL Genome 36:32-42(1993).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7731988; DOI=10.1073/pnas.92.9.3809;
RA Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N.,
RA Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J.,
RA Storms R.K.;
RT "The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995).
RN [6]
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 [7]
RP PROTEIN SEQUENCE OF 2-19, FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=8511969; DOI=10.1002/yea.320090409;
RA Ono B., Ishii N., Naito K., Miyoshi S., Shinoda S., Yamamoto S., Ohmori S.;
RT "Cystathionine gamma-lyase of Saccharomyces cerevisiae: structural gene and
RT cystathionine gamma-synthase activity.";
RL Yeast 9:389-397(1993).
RN [8]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [9]
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 2-393 IN COMPLEX WITH PYRIDOXAL
RP PHOSPHATE, COFACTOR, AND SUBUNIT.
RX PubMed=12715888; DOI=10.1515/bc.2003.043;
RA Messerschmidt A., Worbs M., Steegborn C., Wahl M.C., Huber R., Laber B.,
RA Clausen T.;
RT "Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-
RT dependent enzymes family: crystal structure of cystathionine gamma-lyase
RT from yeast and intrafamiliar structure comparison.";
RL Biol. Chem. 384:373-386(2003).
CC -!- FUNCTION: Catalyzes the production of cysteine from cystathionine in
CC the reverse transsulfuration pathway for the biosynthesis of sulfur-
CC containing amino acids cysteine and methionine. In this pathway,
CC homocysteine sulfur is converted to cysteine sulfur (Probable). Also
CC has cystathionine beta-lyase and cystathionine gamma-synthase
CC activities in vitro. Cystathionine beta-lyase may be physiological,
CC while cystathionine gamma-synthase activity is not, as the required
CC substrate O-succinyl-L-homoserine(OSH) does not occur naturally in
CC S.cerevisiae (PubMed:8335636). {ECO:0000269|PubMed:8335636,
CC ECO:0000305|PubMed:1577698}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L,L-cystathionine = 2-oxobutanoate + L-cysteine +
CC NH4(+); Xref=Rhea:RHEA:14005, ChEBI:CHEBI:15377, ChEBI:CHEBI:16763,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:35235, ChEBI:CHEBI:58161; EC=4.4.1.1;
CC Evidence={ECO:0000269|PubMed:1577698, ECO:0000269|PubMed:8335636,
CC ECO:0000269|PubMed:8511969};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14006;
CC Evidence={ECO:0000269|PubMed:1577698, ECO:0000269|PubMed:8335636,
CC ECO:0000269|PubMed:8511969};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:12715888};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.25 mM for cystathionine (for gamma-lyase reaction)
CC {ECO:0000269|PubMed:8335636};
CC KM=0.5 mM for cystathionine (for beta-lyase reaction)
CC {ECO:0000269|PubMed:8335636};
CC Vmax=0.71 umol/min/mg enzyme (for gamma-lyase reaction)
CC {ECO:0000269|PubMed:8335636};
CC Vmax=0.42 umol/min/mg enzyme (for beta-lyase reaction)
CC {ECO:0000269|PubMed:8335636};
CC -!- PATHWAY: Amino-acid biosynthesis; L-cysteine biosynthesis; L-cysteine
CC from L-homocysteine and L-serine: step 2/2.
CC {ECO:0000305|PubMed:1577698}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:12715888,
CC ECO:0000269|PubMed:8335636}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 38300 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the trans-sulfuration enzymes family.
CC {ECO:0000305}.
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DR EMBL; L05146; AAC04945.1; -; Genomic_DNA.
DR EMBL; D14135; BAA03190.1; -; Genomic_DNA.
DR EMBL; BK006935; DAA06976.1; -; Genomic_DNA.
DR PIR; S31228; S31228.
DR RefSeq; NP_009390.1; NM_001178157.1.
DR PDB; 1N8P; X-ray; 2.60 A; A/B/C/D=2-394.
DR PDBsum; 1N8P; -.
DR AlphaFoldDB; P31373; -.
DR SMR; P31373; -.
DR BioGRID; 31754; 236.
DR DIP; DIP-4440N; -.
DR IntAct; P31373; 7.
DR MINT; P31373; -.
DR STRING; 4932.YAL012W; -.
DR iPTMnet; P31373; -.
DR MaxQB; P31373; -.
DR PaxDb; P31373; -.
DR PRIDE; P31373; -.
DR EnsemblFungi; YAL012W_mRNA; YAL012W; YAL012W.
DR GeneID; 851221; -.
DR KEGG; sce:YAL012W; -.
DR SGD; S000000010; CYS3.
DR VEuPathDB; FungiDB:YAL012W; -.
DR eggNOG; KOG0053; Eukaryota.
DR GeneTree; ENSGT00390000000312; -.
DR HOGENOM; CLU_018986_2_3_1; -.
DR InParanoid; P31373; -.
DR OMA; YKQDGVG; -.
DR BioCyc; MetaCyc:YAL012W-MON; -.
DR BioCyc; YEAST:YAL012W-MON; -.
DR BRENDA; 4.4.1.1; 984.
DR Reactome; R-SCE-1614558; Degradation of cysteine and homocysteine.
DR Reactome; R-SCE-1614603; Cysteine formation from homocysteine.
DR UniPathway; UPA00136; UER00202.
DR EvolutionaryTrace; P31373; -.
DR PRO; PR:P31373; -.
DR Proteomes; UP000002311; Chromosome I.
DR RNAct; P31373; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0016846; F:carbon-sulfur lyase activity; IBA:GO_Central.
DR GO; GO:0004123; F:cystathionine gamma-lyase activity; IDA:SGD.
DR GO; GO:0047804; F:cysteine-S-conjugate beta-lyase activity; IDA:SGD.
DR GO; GO:0080146; F:L-cysteine desulfhydrase activity; IEA:UniProtKB-EC.
DR GO; GO:0044540; F:L-cystine L-cysteine-lyase (deaminating); IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0019344; P:cysteine biosynthetic process; IMP:SGD.
DR GO; GO:0019343; P:cysteine biosynthetic process via cystathionine; IMP:SGD.
DR GO; GO:1904828; P:positive regulation of hydrogen sulfide biosynthetic process; IDA:SGD.
DR GO; GO:0019346; P:transsulfuration; IMP:SGD.
DR CDD; cd00614; CGS_like; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000277; Cys/Met-Metab_PyrdxlP-dep_enz.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR11808; PTHR11808; 1.
DR Pfam; PF01053; Cys_Met_Meta_PP; 1.
DR PIRSF; PIRSF001434; CGS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00868; CYS_MET_METAB_PP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cysteine biosynthesis; Cytoplasm;
KW Direct protein sequencing; Lyase; Phosphoprotein; Pyridoxal phosphate;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8511969"
FT CHAIN 2..394
FT /note="Cystathionine gamma-lyase"
FT /id="PRO_0000114754"
FT REGION 37..57
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 52
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 104
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 109
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 334
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 204
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT MOD_RES 362
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT HELIX 9..15
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 38..47
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 56..68
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 72..78
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 96..102
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 105..113
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 128..135
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 138..145
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 158..168
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 169..173
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 175..179
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 196..201
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 202..207
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 222..235
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 241..251
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 254..272
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 276..278
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 279..283
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 293..299
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 307..315
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 317..326
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 328..332
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 346..350
FT /evidence="ECO:0007829|PDB:1N8P"
FT TURN 356..360
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 361..363
FT /evidence="ECO:0007829|PDB:1N8P"
FT STRAND 368..372
FT /evidence="ECO:0007829|PDB:1N8P"
FT HELIX 378..393
FT /evidence="ECO:0007829|PDB:1N8P"
SQ SEQUENCE 394 AA; 42542 MW; 861A5AA7557687FC CRC64;
MTLQESDKFA TKAIHAGEHV DVHGSVIEPI SLSTTFKQSS PANPIGTYEY SRSQNPNREN
LERAVAALEN AQYGLAFSSG SATTATILQS LPQGSHAVSI GDVYGGTHRY FTKVANAHGV
ETSFTNDLLN DLPQLIKENT KLVWIETPTN PTLKVTDIQK VADLIKKHAA GQDVILVVDN
TFLSPYISNP LNFGADIVVH SATKYINGHS DVVLGVLATN NKPLYERLQF LQNAIGAIPS
PFDAWLTHRG LKTLHLRVRQ AALSANKIAE FLAADKENVV AVNYPGLKTH PNYDVVLKQH
RDALGGGMIS FRIKGGAEAA SKFASSTRLF TLAESLGGIE SLLEVPAVMT HGGIPKEARE
ASGVFDDLVR ISVGIEDTDD LLEDIKQALK QATN
