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   02-SEP-2026, entry version 180.
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:0000269|PubMed:11402193, 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), FUNCTION, 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   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [5]
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   [6]
RP   X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-464, FUNCTION, CATALYTIC
RP   ACTIVITY, COFACTOR, SUBUNIT, AND PYRIDOXAL 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).
RN   [7]
RP   FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=31002461; DOI=10.1111/tpj.14343;
RA   Liu G., Yang W., Zhang X., Peng T., Zou Y., Zhang T., Wang H., Liu X.,
RA   Tao L.Z.;
RT   "Cystathionine beta-lyase is crucial for embryo patterning and the
RT   maintenance of root stem cell niche in Arabidopsis.";
RL   Plant J. 99:536-555(2019).
RN   [8]
RP   FUNCTION.
RX   PubMed=35472754; DOI=10.1016/j.plaphy.2022.04.008;
RA   Wang Z., He F., Mu Y., Zhang L., Liu Z., Liu D., Yang J., Jin Z., Pei Y.;
RT   "Identification and functional characterization of a cystathionine beta-
RT   lyase (CBL) enzyme for H2S production in Arabidopsis thaliana.";
RL   Plant Physiol. Biochem. 182:76-89(2022).
CC   -!- FUNCTION: Catalyzes the penultimate step in the de novo biosynthesis of
CC       methionine (PubMed:11402193, PubMed:31002461, PubMed:8541513). Its role
CC       in methionine metabolism may affect plant development in different
CC       organs, probably by modifying plant auxin transport (PubMed:31002461).
CC       Its cysteine desulfhydrase activity may be involved in hydrogen sulfur
CC       production using L-cysteine as a substrate (PubMed:35472754).
CC       {ECO:0000269|PubMed:11402193, ECO:0000269|PubMed:31002461,
CC       ECO:0000269|PubMed:35472754, ECO:0000269|PubMed:8541513}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L,L-cystathionine + H2O = L-homocysteine + pyruvate + NH4(+);
CC         Xref=Rhea:RHEA:13965, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:28938, ChEBI:CHEBI:58161, ChEBI:CHEBI:58199;
CC         Evidence={ECO:0000269|PubMed:11402193, ECO:0000305|PubMed:8541513};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13966;
CC         Evidence={ECO:0000305|PubMed:11402193};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=an S-substituted L-cysteine + H2O = a thiol + pyruvate +
CC         NH4(+); 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         Evidence={ECO:0000269|PubMed:11402193, ECO:0000305|PubMed:8541513};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000269|PubMed:11402193};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo
CC       pathway; L-homocysteine from L-cystathionine: step 1/1.
CC   -!- SUBUNIT: Forms homodimers (PubMed:11402193). May form homotetramers
CC       from two homodimers (PubMed:11402193). {ECO:0000269|PubMed:11402193}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC       {ECO:0000269|PubMed:31002461}.
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   -!- DISRUPTION PHENOTYPE: Decreased abundance of several PIN-FORMED (PIN)
CC       proteins, involved in plant auxin transport, and impaired auxin-
CC       responsive gene expression. {ECO:0000269|PubMed:31002461}.
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; OZ408685; CAO7044757.1; -; Genomic_DNA.
DR   EMBL; OZ408685; CAO7044758.1; -; Genomic_DNA.
DR   EMBL; AY064018; AAL36374.1; -; mRNA.
DR   EMBL; AY114051; AAM45099.1; -; mRNA.
DR   PIR; S61429; S61429.
DR   PDB; 1IBJ; X-ray; 2.30 A; A/C=1-464.
DR   AlphaFoldDB; P53780; -.
DR   SMR; P53780; -.
DR   BioGRID; 10188; 3.
DR   FunCoup; P53780; 1786.
DR   IntAct; P53780; 2.
DR   STRING; 3702.P53780; -.
DR   MetOSite; P53780; -.
DR   PaxDb; 3702-P53780; -.
DR   KEGG; ath:AT3G57050; -.
DR   Araport; AT3G57050; -.
DR   TAIR; AT3G57050; CBL.
DR   eggNOG; KOG0053; Eukaryota.
DR   InParanoid; P53780; -.
DR   OrthoDB; 3512640at2759; -.
DR   PhylomeDB; P53780; -.
DR   BioCyc; ARA:AT3G57050-MONOMER; -.
DR   BioCyc; MetaCyc:AT3G57050-MONOMER; -.
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   GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR   GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR   GO; GO:0005737; C:cytoplasm; ISM:TAIR.
DR   GO; GO:0047804; F:cysteine-S-conjugate beta-lyase activity; IDA:UniProtKB.
DR   GO; GO:0060090; F:molecular adaptor activity; EXP:DisProt.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR   GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR   GO; GO:0071265; P:L-methionine biosynthetic process; IDA:UniProtKB.
DR   GO; GO:0019346; P:transsulfuration; IBA:GO_Central.
DR   CDD; cd00614; CGS_like; 1.
DR   DisProt; DP02642; -.
DR   FunFam; 3.90.1150.10:FF:000013; Cystathionine beta-lyase; 1.
DR   FunFam; 3.40.640.10:FF:000009; Cystathionine gamma-synthase homolog; 1.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR   InterPro; IPR000277; Cys/Met-Metab_PyrdxlP-dep_enz.
DR   InterPro; IPR006238; Cys_b_lyase_euk.
DR   InterPro; IPR054542; Cys_met_metab_PP.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR   NCBIfam; TIGR01329; cysta_beta_ly_E; 1.
DR   PANTHER; PTHR11808:SF50; CYSTATHIONINE BETA-LYASE; 1.
DR   PANTHER; PTHR11808; TRANS-SULFURATION ENZYME FAMILY MEMBER; 1.
DR   Pfam; PF01053; Cys_Met_Meta_PP; 1.
DR   PIRSF; PIRSF001434; CGS; 1.
DR   SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR   PROSITE; PS00868; CYS_MET_METAB_PP; 1.
DR   PDBsum; 1IBJ; -.
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..55
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           56..464
FT                   /note="Cystathionine beta-lyase, chloroplastic"
FT                   /id="PRO_0000033454"
FT   BINDING         127
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   BINDING         129
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   BINDING         157
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   BINDING         158
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   BINDING         275
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   BINDING         277
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
FT   MOD_RES         278
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000269|PubMed:11402193,
FT                   ECO:0007744|PDB:1IBJ"
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   HELIX           106..108
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..186
FT                   /evidence="ECO:0007829|PDB:1IBJ"
FT   HELIX           187..191
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
//