CBBY_ARATH
ID CBBY_ARATH Reviewed; 319 AA.
AC Q94K71; Q67ZZ0; Q8LCE8; Q9STM2;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=CBBY-like protein {ECO:0000303|PubMed:27246049};
DE Short=AtCbby {ECO:0000303|PubMed:27246049};
DE EC=3.1.3.- {ECO:0000269|PubMed:27246049};
DE Flags: Precursor;
GN Name=CBBY {ECO:0000303|PubMed:27246049};
GN OrderedLocusNames=At3g48420 {ECO:0000312|Araport:AT3G48420};
GN ORFNames=T29H11.60 {ECO:0000312|EMBL:CAB41156.1};
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7] {ECO:0007744|PDB:4UAV}
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 74-319 IN COMPLEX WITH MAGNESIUM,
RP CATALYTIC ACTIVITY, COFACTOR, FUNCTION, SUBSTRATE SPECIFICITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF ASP-84; GLU-91; HIS-95;
RP TYR-117; ARG-129 AND LYS-161.
RX PubMed=27246049; DOI=10.1038/nplants.2014.2;
RA Bracher A., Sharma A., Starling-Windhof A., Hartl F.U., Hayer-Hartl M.;
RT "Degradation of potent Rubisco inhibitor by selective sugar phosphatase.";
RL Nat. Plants 1:14002-14002(2015).
CC -!- FUNCTION: Highly selective xylulose-1,5-bisphosphate (XuBP)
CC phosphatase. Shows also activity towards ribulose-1,5-bisphosphate
CC (RuBP) and fructose-1,6-bisphosphate (FBP), but not towards fructose-6-
CC phosphate (F6P) or ribulose-5-phosphate (Ru5P) (PubMed:27246049).
CC Degrades xylulose-1,5-bisphosphate, a potent inhibitor of rubisco
CC produced by the rubisco itself (PubMed:27246049).
CC {ECO:0000269|PubMed:27246049}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-xylulose 1,5-bisphosphate + H2O = D-xylulose 5-phosphate +
CC phosphate; Xref=Rhea:RHEA:54548, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57737, ChEBI:CHEBI:138268;
CC Evidence={ECO:0000269|PubMed:27246049};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27246049};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.033 mM for xylulose-1,5-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC KM=3.06 mM for ribulose-1,5-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC KM=6.2 mM for fructose-1,6-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC Note=kcat is 2.45 sec(-1) with xylulose-1,5-bisphosphate as
CC substrate. kcat is 0.049 sec(-1) with ribulose-1,5-bisphosphate as
CC substrate. {ECO:0000269|PubMed:27246049};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. DOG/GPP
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB41156.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At3g48420 and At3g48425.; Evidence={ECO:0000305};
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DR EMBL; AL049659; CAB41156.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78414.1; -; Genomic_DNA.
DR EMBL; AF370250; AAK44065.1; -; mRNA.
DR EMBL; AY063066; AAL34240.1; -; mRNA.
DR EMBL; AK118118; BAC42744.1; -; mRNA.
DR EMBL; AK175866; BAD43629.1; -; mRNA.
DR EMBL; AK175977; BAD43740.1; -; mRNA.
DR EMBL; AK176795; BAD44558.1; -; mRNA.
DR EMBL; AY086642; AAM63700.1; -; mRNA.
DR PIR; T06700; T06700.
DR RefSeq; NP_566903.1; NM_114701.3.
DR PDB; 4UAV; X-ray; 1.30 A; A=74-319.
DR PDBsum; 4UAV; -.
DR AlphaFoldDB; Q94K71; -.
DR SMR; Q94K71; -.
DR STRING; 3702.AT3G48420.1; -.
DR MetOSite; Q94K71; -.
DR PaxDb; Q94K71; -.
DR PRIDE; Q94K71; -.
DR ProteomicsDB; 223926; -.
DR EnsemblPlants; AT3G48420.1; AT3G48420.1; AT3G48420.
DR GeneID; 824000; -.
DR Gramene; AT3G48420.1; AT3G48420.1; AT3G48420.
DR KEGG; ath:AT3G48420; -.
DR Araport; AT3G48420; -.
DR TAIR; locus:2101165; AT3G48420.
DR eggNOG; KOG2914; Eukaryota.
DR HOGENOM; CLU_045011_0_0_1; -.
DR InParanoid; Q94K71; -.
DR OMA; LEGVYWD; -.
DR OrthoDB; 747123at2759; -.
DR PhylomeDB; Q94K71; -.
DR PRO; PR:Q94K71; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q94K71; baseline and differential.
DR Genevisible; Q94K71; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR044999; CbbY-like.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR PANTHER; PTHR42896; PTHR42896; 1.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Hydrolase; Magnesium; Metal-binding; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..65
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 66..319
FT /note="CBBY-like protein"
FT /id="PRO_0000424321"
FT ACT_SITE 82
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:27246049"
FT ACT_SITE 84
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:27246049"
FT BINDING 82
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAV"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 84
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAV"
FT BINDING 91
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 125..129
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 158..161
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 198..204
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 258
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAV"
FT MUTAGEN 84
FT /note="D->N: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 91
FT /note="E->A: 40% to 80% decreased catalytic activity with
FT xylulose-1,5-bisphosphate, but no effect on activity with
FT ribulose-1,5-bisphosphate."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 95
FT /note="H->A: 40% to 80% decreased catalytic activity with
FT xylulose-1,5-bisphosphate, but no effect on activity with
FT ribulose-1,5-bisphosphate."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 117
FT /note="Y->A: 40% to 80% decreased catalytic activity with
FT xylulose-1,5-bisphosphate, but no effect on activity with
FT ribulose-1,5-bisphosphate."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 129
FT /note="R->A: 97% decreased catalytic activity with
FT xylulose-1,5-bisphosphate, but no effect on activity with
FT ribulose-1,5-bisphosphate."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 161
FT /note="K->A: 40% to 80% decreased catalytic activity with
FT xylulose-1,5-bisphosphate, but no effect on activity with
FT ribulose-1,5-bisphosphate."
FT /evidence="ECO:0000269|PubMed:27246049"
FT CONFLICT 106
FT /note="R -> G (in Ref. 5; BAD43740)"
FT /evidence="ECO:0000305"
FT CONFLICT 314
FT /note="R -> Q (in Ref. 6; AAM63700)"
FT /evidence="ECO:0000305"
FT STRAND 77..81
FT /evidence="ECO:0007829|PDB:4UAV"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 90..93
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 114..120
FT /evidence="ECO:0007829|PDB:4UAV"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 126..137
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 147..170
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 180..189
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 202..212
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 215..218
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 221..224
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 237..246
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 250..252
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 260..268
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:4UAV"
FT TURN 279..283
FT /evidence="ECO:0007829|PDB:4UAV"
FT STRAND 290..294
FT /evidence="ECO:0007829|PDB:4UAV"
FT HELIX 306..312
FT /evidence="ECO:0007829|PDB:4UAV"
SQ SEQUENCE 319 AA; 34246 MW; DEBCA30D027CFCD6 CRC64;
MATVKISLSL ASLSPSSSSS SIQSKLSPSF IPNAAPAKAV KLRFNGKSLR AKPMVYRSSR
SVGVTCSASS SLTTLPSALL FDCDGVLVDT EKDGHRISFN DTFKERDLNV TWDVDLYGEL
LKIGGGKERM TAYFNKVGWP EKAPKDEAER KEFIAGLHKQ KTELFMVLIE KKLLPLRPGV
AKLVDQALTN GVKVAVCSTS NEKAVSAIVS CLLGPERAEK IKIFAGDVVP KKKPDPAIYN
LAAETLGVDP SKCVVVEDSA IGLAAAKAAG MTCIVTKSGY TADEDFENAD AVFDCIGDPP
EERFDLAFCG SLLRKQFVS
