CBBY_CERSP
ID CBBY_CERSP Reviewed; 230 AA.
AC P95649;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=Protein CbbY {ECO:0000303|PubMed:9006018};
DE Short=RuCbby {ECO:0000303|PubMed:9006018};
DE EC=3.1.3.- {ECO:0000269|PubMed:27246049};
GN Name=cbbY {ECO:0000303|PubMed:9006018};
OS Cereibacter sphaeroides (Rhodobacter sphaeroides).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Cereibacter.
OX NCBI_TaxID=1063;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=HR;
RX PubMed=9006018; DOI=10.1128/jb.179.3.663-669.1997;
RA Gibson J.L., Tabita F.R.;
RT "Analysis of the cbbXYZ operon in Rhodobacter sphaeroides.";
RL J. Bacteriol. 179:663-669(1997).
RN [2] {ECO:0007744|PDB:4UAR, ECO:0007744|PDB:4UAS, ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU}
RP X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
RP SUBSTRATE, CATALYTIC ACTIVITY, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF ASP-10; GLU-17; HIS-20; TYR-42; ARG-54 AND LYS-78.
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=0.026 mM for xylulose-1,5-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC KM=2.9 mM for ribulose-1,5-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC KM=5.0 mM for fructose-1,6-bisphosphate
CC {ECO:0000269|PubMed:27246049};
CC Note=kcat is 2.4 sec(-1) with xylulose-1,5-bisphosphate as substrate.
CC kcat is 0.042 sec(-1) with ribulose-1,5-bisphosphate as substrate.
CC {ECO:0000269|PubMed:27246049};
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC CbbY/CbbZ/Gph/YieH family. {ECO:0000305}.
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DR EMBL; U67781; AAC44828.1; -; Genomic_DNA.
DR RefSeq; WP_002721822.1; NZ_WSNV01000001.1.
DR PDB; 4UAR; X-ray; 1.90 A; A=1-230.
DR PDB; 4UAS; X-ray; 1.20 A; A/B=1-230.
DR PDB; 4UAT; X-ray; 1.30 A; A/B=1-230.
DR PDB; 4UAU; X-ray; 1.45 A; A/B=1-230.
DR PDBsum; 4UAR; -.
DR PDBsum; 4UAS; -.
DR PDBsum; 4UAT; -.
DR PDBsum; 4UAU; -.
DR AlphaFoldDB; P95649; -.
DR SMR; P95649; -.
DR GeneID; 57471609; -.
DR GeneID; 67448050; -.
DR OMA; LEGVYWD; -.
DR OrthoDB; 1167152at2; -.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0005998; P:xylulose catabolic process; IDA:UniProtKB.
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 PRINTS; PR00413; HADHALOGNASE.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding.
FT CHAIN 1..230
FT /note="Protein CbbY"
FT /id="PRO_0000108057"
FT ACT_SITE 8
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:27246049"
FT ACT_SITE 10
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:27246049"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAS"
FT BINDING 8
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU"
FT BINDING 10
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAS"
FT BINDING 17
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU"
FT BINDING 50..54
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU"
FT BINDING 75..78
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU"
FT BINDING 115..121
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:4UAT, ECO:0007744|PDB:4UAU"
FT BINDING 176
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0007744|PDB:4UAS"
FT MUTAGEN 10
FT /note="D->N: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:27246049"
FT MUTAGEN 17
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 20
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 42
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 54
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 78
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 STRAND 4..7
FT /evidence="ECO:0007829|PDB:4UAS"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 17..31
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 39..45
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 51..61
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 71..87
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 97..107
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 110..114
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 119..129
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 155..164
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 171..177
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 178..186
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:4UAS"
FT TURN 197..201
FT /evidence="ECO:0007829|PDB:4UAS"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:4UAS"
FT HELIX 220..223
FT /evidence="ECO:0007829|PDB:4UAS"
SQ SEQUENCE 230 AA; 25119 MW; 811BD8FE22A76918 CRC64;
MIEAILFDVD GTLAETEELH RRAFNETFAA LGVDWFWDRE EYRELLTTTG GKERIARFLR
HQKGDPAPLP IADIHRAKTE RFVALMAEGE IALRPGIADL IAEAKRAGIR LAVATTTSLP
NVEALCRACF GHPAREIFDV IAAGDMVAEK KPSPDIYRLA LRELDVPPER AVALEDSLNG
LRAAKGAGLR CIVSPGFYTR HEEFAGADRL LDSFAELGGL AGLDLTAPVA
