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Protein CbbY (RuCbby) (EC 3.1.3.-)

 CBBY_RHOSH              Reviewed;         230 AA.
P95649;
15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
01-MAY-1997, sequence version 1.
28-MAR-2018, entry version 66.
RecName: Full=Protein CbbY {ECO:0000303|PubMed:9006018};
Short=RuCbby {ECO:0000303|PubMed:9006018};
EC=3.1.3.- {ECO:0000269|PubMed:27246049};
Name=cbbY {ECO:0000303|PubMed:9006018};
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides).
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
Rhodobacteraceae; Rhodobacter.
NCBI_TaxID=1063;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=HR;
PubMed=9006018; DOI=10.1128/jb.179.3.663-669.1997;
Gibson J.L., Tabita F.R.;
"Analysis of the cbbXYZ operon in Rhodobacter sphaeroides.";
J. Bacteriol. 179:663-669(1997).
[2] {ECO:0000244|PDB:4UAR, ECO:0000244|PDB:4UAS, ECO:0000244|PDB:4UAT, ECO:0000244|PDB:4UAU}
X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
SUBSTRATE, CATALYTIC ACTIVITY, FUNCTION, BIOPHYSICOCHEMICAL
PROPERTIES, AND MUTAGENESIS OF ASP-10; GLU-17; HIS-20; TYR-42; ARG-54
AND LYS-78.
PubMed=27246049; DOI=10.1038/nplants.2014.2;
Bracher A., Sharma A., Starling-Windhof A., Hartl F.U.,
Hayer-Hartl M.;
"Degradation of potent Rubisco inhibitor by selective sugar
phosphatase.";
Nat. Plants 1:14002-14002(2015).
-!- FUNCTION: Highly selective xylulose-1,5-bisphosphate (XuBP)
phosphatase. Shows also activity towards ribulose-1,5-bisphosphate
(RuBP) and fructose-1,6-bisphosphate (FBP), but not towards
fructose-6-phosphate (F6P) or ribulose-5-phosphate (Ru5P)
(PubMed:27246049). Degrades xylulose-1,5-bisphosphate, a potent
inhibitor of rubisco produced by the rubisco itself
(PubMed:27246049). {ECO:0000269|PubMed:27246049}.
-!- CATALYTIC ACTIVITY: Xylulose-1,5-bisphosphate + H(2)O = xylulose
5-phosphate + phosphate. {ECO:0000269|PubMed:27246049}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:27246049};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.026 mM for xylulose-1,5-bisphosphate
{ECO:0000269|PubMed:27246049};
KM=2.9 mM for ribulose-1,5-bisphosphate
{ECO:0000269|PubMed:27246049};
KM=5.0 mM for fructose-1,6-bisphosphate
{ECO:0000269|PubMed:27246049};
Note=kcat is 2.4 sec(-1) with xylulose-1,5-bisphosphate as
substrate. kcat is 0.042 sec(-1) with ribulose-1,5-bisphosphate
as substrate. {ECO:0000269|PubMed:27246049};
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CbbY/CbbZ/Gph/YieH family. {ECO:0000305}.
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EMBL; U67781; AAC44828.1; -; Genomic_DNA.
RefSeq; WP_002721822.1; NZ_CP015287.1.
PDB; 4UAR; X-ray; 1.90 A; A=1-230.
PDB; 4UAS; X-ray; 1.20 A; A/B=1-230.
PDB; 4UAT; X-ray; 1.30 A; A/B=1-230.
PDB; 4UAU; X-ray; 1.45 A; A/B=1-230.
PDBsum; 4UAR; -.
PDBsum; 4UAS; -.
PDBsum; 4UAT; -.
PDBsum; 4UAU; -.
ProteinModelPortal; P95649; -.
SMR; P95649; -.
eggNOG; ENOG4107S75; Bacteria.
eggNOG; COG0637; LUCA.
GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008152; P:metabolic process; IEA:InterPro.
Gene3D; 1.10.150.240; -; 1.
Gene3D; 3.40.50.1000; -; 2.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006439; HAD-SF_hydro_IA.
InterPro; IPR023214; HAD_sf.
InterPro; IPR023198; PGP-like_dom2.
PRINTS; PR00413; HADHALOGNASE.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
1: Evidence at protein level;
3D-structure; Hydrolase; Magnesium; Metal-binding.
CHAIN 1 230 Protein CbbY.
/FTId=PRO_0000108057.
REGION 50 54 Substrate binding. {ECO:0000244|PDB:4UAT,
ECO:0000244|PDB:4UAU}.
REGION 75 78 Substrate binding. {ECO:0000244|PDB:4UAT,
ECO:0000244|PDB:4UAU}.
REGION 115 121 Substrate binding. {ECO:0000244|PDB:4UAT,
ECO:0000244|PDB:4UAU}.
ACT_SITE 8 8 Nucleophile.
{ECO:0000305|PubMed:27246049}.
ACT_SITE 10 10 Proton donor.
{ECO:0000305|PubMed:27246049}.
METAL 8 8 Magnesium. {ECO:0000244|PDB:4UAS}.
METAL 10 10 Magnesium; via carbonyl oxygen.
{ECO:0000244|PDB:4UAS}.
METAL 176 176 Magnesium. {ECO:0000244|PDB:4UAS}.
BINDING 8 8 Substrate. {ECO:0000244|PDB:4UAT,
ECO:0000244|PDB:4UAU}.
BINDING 17 17 Substrate. {ECO:0000244|PDB:4UAT,
ECO:0000244|PDB:4UAU}.
MUTAGEN 10 10 D->N: Loss of catalytic activity.
{ECO:0000269|PubMed:27246049}.
MUTAGEN 17 17 E->A: 40% to 80% decreased catalytic
activity with xylulose-1,5-bisphosphate,
but no effect on activity with ribulose-
1,5-bisphosphate.
{ECO:0000269|PubMed:27246049}.
MUTAGEN 20 20 H->A: 40% to 80% decreased catalytic
activity with xylulose-1,5-bisphosphate,
but no effect on activity with ribulose-
1,5-bisphosphate.
{ECO:0000269|PubMed:27246049}.
MUTAGEN 42 42 Y->A: 40% to 80% decreased catalytic
activity with xylulose-1,5-bisphosphate,
but no effect on activity with ribulose-
1,5-bisphosphate.
{ECO:0000269|PubMed:27246049}.
MUTAGEN 54 54 R->A: 97% decreased catalytic activity
with xylulose-1,5-bisphosphate, but no
effect on activity with ribulose-1,5-
bisphosphate.
{ECO:0000269|PubMed:27246049}.
MUTAGEN 78 78 K->A: 40% to 80% decreased catalytic
activity with xylulose-1,5-bisphosphate,
but no effect on activity with ribulose-
1,5-bisphosphate.
{ECO:0000269|PubMed:27246049}.
STRAND 4 7 {ECO:0000244|PDB:4UAS}.
TURN 10 12 {ECO:0000244|PDB:4UAS}.
HELIX 17 31 {ECO:0000244|PDB:4UAS}.
HELIX 39 45 {ECO:0000244|PDB:4UAS}.
HELIX 51 61 {ECO:0000244|PDB:4UAS}.
HELIX 71 87 {ECO:0000244|PDB:4UAS}.
HELIX 97 107 {ECO:0000244|PDB:4UAS}.
STRAND 110 114 {ECO:0000244|PDB:4UAS}.
HELIX 119 129 {ECO:0000244|PDB:4UAS}.
HELIX 134 136 {ECO:0000244|PDB:4UAS}.
STRAND 139 142 {ECO:0000244|PDB:4UAS}.
HELIX 144 146 {ECO:0000244|PDB:4UAS}.
STRAND 147 149 {ECO:0000244|PDB:4UAS}.
HELIX 155 164 {ECO:0000244|PDB:4UAS}.
HELIX 168 170 {ECO:0000244|PDB:4UAS}.
STRAND 171 177 {ECO:0000244|PDB:4UAS}.
HELIX 178 186 {ECO:0000244|PDB:4UAS}.
STRAND 190 193 {ECO:0000244|PDB:4UAS}.
TURN 197 201 {ECO:0000244|PDB:4UAS}.
STRAND 208 210 {ECO:0000244|PDB:4UAS}.
HELIX 214 216 {ECO:0000244|PDB:4UAS}.
HELIX 220 223 {ECO:0000244|PDB:4UAS}.
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


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