METC_ARATH
ID METC_ARATH Reviewed; 464 AA.
AC P53780; Q8VZL8;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Cystathionine beta-lyase, chloroplastic {ECO:0000303|PubMed:8541513};
DE Short=CBL {ECO:0000303|PubMed:8541513};
DE EC=4.4.1.13 {ECO:0000305|PubMed:8541513};
DE AltName: Full=Beta-cystathionase;
DE AltName: Full=Cysteine lyase;
DE AltName: Full=Cysteine-S-conjugate beta-lyase;
DE Flags: Precursor;
GN OrderedLocusNames=At3g57050; ORFNames=F24I3.130;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=8541513; DOI=10.1007/bf00041177;
RA Ravanel S., Ruffet M.L., Douce R.;
RT "Cloning of an Arabidopsis thaliana cDNA encoding cystathionine beta-lyase
RT by functional complementation in Escherichia coli.";
RL Plant Mol. Biol. 29:875-882(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 85-464, SUBUNIT, AND PYRIDOXAL
RP PHOSPHATE AT LYS-278.
RX PubMed=11402193; DOI=10.1104/pp.126.2.631;
RA Breitinger U., Clausen T., Ehlert S., Huber R., Laber B., Schmidt F.,
RA Pohl E., Messerschmidt A.;
RT "The three-dimensional structure of cystathionine beta-lyase from
RT Arabidopsis and its substrate specificity.";
RL Plant Physiol. 126:631-642(2001).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L,L-cystathionine = L-homocysteine + NH4(+) + pyruvate;
CC Xref=Rhea:RHEA:13965, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58161, ChEBI:CHEBI:58199;
CC Evidence={ECO:0000305|PubMed:8541513};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an S-substituted L-cysteine + H2O = a thiol + NH4(+) +
CC pyruvate; Xref=Rhea:RHEA:18121, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:29256, ChEBI:CHEBI:58717; EC=4.4.1.13;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC pathway; L-homocysteine from L-cystathionine: step 1/1.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:11402193}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=P53780-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P53780-2; Sequence=VSP_008894;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the trans-sulfuration enzymes family.
CC {ECO:0000305}.
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DR EMBL; L40511; AAA99176.1; -; mRNA.
DR EMBL; AL138655; CAB72175.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79603.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79605.1; -; Genomic_DNA.
DR EMBL; AY064018; AAL36374.1; -; mRNA.
DR EMBL; AY114051; AAM45099.1; -; mRNA.
DR PIR; S61429; S61429.
DR RefSeq; NP_191264.1; NM_115564.4. [P53780-1]
DR RefSeq; NP_850712.1; NM_180381.3. [P53780-2]
DR PDB; 1IBJ; X-ray; 2.30 A; A/C=1-464.
DR PDBsum; 1IBJ; -.
DR AlphaFoldDB; P53780; -.
DR SMR; P53780; -.
DR BioGRID; 10188; 3.
DR IntAct; P53780; 2.
DR STRING; 3702.AT3G57050.1; -.
DR PaxDb; P53780; -.
DR PRIDE; P53780; -.
DR EnsemblPlants; AT3G57050.1; AT3G57050.1; AT3G57050. [P53780-1]
DR EnsemblPlants; AT3G57050.2; AT3G57050.2; AT3G57050. [P53780-2]
DR GeneID; 824872; -.
DR Gramene; AT3G57050.1; AT3G57050.1; AT3G57050. [P53780-1]
DR Gramene; AT3G57050.2; AT3G57050.2; AT3G57050. [P53780-2]
DR KEGG; ath:AT3G57050; -.
DR Araport; AT3G57050; -.
DR TAIR; locus:2080605; AT3G57050.
DR eggNOG; KOG0053; Eukaryota.
DR InParanoid; P53780; -.
DR PhylomeDB; P53780; -.
DR BioCyc; ARA:AT3G57050-MON; -.
DR BioCyc; MetaCyc:AT3G57050-MON; -.
DR BRENDA; 4.4.1.13; 399.
DR SABIO-RK; P53780; -.
DR UniPathway; UPA00051; UER00078.
DR EvolutionaryTrace; P53780; -.
DR PRO; PR:P53780; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; P53780; baseline and differential.
DR Genevisible; P53780; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016846; F:carbon-sulfur lyase activity; IBA:GO_Central.
DR GO; GO:0004121; F:cystathionine beta-lyase activity; IMP:TAIR.
DR GO; GO:0004123; F:cystathionine gamma-lyase activity; IBA:GO_Central.
DR GO; GO:0047804; F:cysteine-S-conjugate beta-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0019343; P:cysteine biosynthetic process via cystathionine; IBA:GO_Central.
DR GO; GO:0019279; P:L-methionine biosynthetic process from L-homoserine via cystathionine; TAS:TAIR.
DR GO; GO:0019346; P:transsulfuration; IBA:GO_Central.
DR CDD; cd00614; CGS_like; 1.
DR DisProt; DP02642; -.
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; IPR006238; Cys_b_lyase_euk.
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 TIGRFAMs; TIGR01329; cysta_beta_ly_E; 1.
DR PROSITE; PS00868; CYS_MET_METAB_PP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Amino-acid biosynthesis; Chloroplast;
KW Lyase; Methionine biosynthesis; Plastid; Pyridoxal phosphate;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN ?..464
FT /note="Cystathionine beta-lyase, chloroplastic"
FT /id="PRO_0000033454"
FT MOD_RES 278
FT /note="N6-(pyridoxal phosphate)lysine"
FT VAR_SEQ 63..78
FT /note="GQTHSTVNNTTDSLNT -> A (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_008894"
FT HELIX 87..91
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 133..146
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 157..165
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 198..202
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 207..213
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 216..223
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 228..230
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 236..244
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 245..247
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 249..253
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 255..257
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 270..275
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 276..281
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 296..308
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 315..325
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 328..347
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 354..356
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 366..369
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 370..372
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 378..383
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 387..396
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 398..402
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 408..410
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 412..414
FT /evidence="ECO:0007829|PDB:1IBJ"
FT TURN 416..421
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 426..433
FT /evidence="ECO:0007829|PDB:1IBJ"
FT STRAND 439..442
FT /evidence="ECO:0007829|PDB:1IBJ"
FT HELIX 448..460
FT /evidence="ECO:0007829|PDB:1IBJ"
SQ SEQUENCE 464 AA; 50430 MW; DE756848549D2CA6 CRC64;
MTSSLSLHSS FVPSFADLSD RGLISKNSPT SVSISKVPTW EKKQISNRNS FKLNCVMEKS
VDGQTHSTVN NTTDSLNTMN IKEEASVSTL LVNLDNKFDP FDAMSTPLYQ TATFKQPSAI
ENGPYDYTRS GNPTRDALES LLAKLDKADR AFCFTSGMAA LSAVTHLIKN GEEIVAGDDV
YGGSDRLLSQ VVPRSGVVVK RVNTTKLDEV AAAIGPQTKL VWLESPTNPR QQISDIRKIS
EMAHAQGALV LVDNSIMSPV LSRPLELGAD IVMHSATKFI AGHSDVMAGV LAVKGEKLAK
EVYFLQNSEG SGLAPFDCWL CLRGIKTMAL RIEKQQENAR KIAMYLSSHP RVKKVYYAGL
PDHPGHHLHF SQAKGAGSVF SFITGSVALS KHLVETTKYF SIAVSFGSVK SLISMPCFMS
HASIPAEVRE ARGLTEDLVR ISAGIEDVDD LISDLDIAFK TFPL
