KDGGP_BACTN
ID KDGGP_BACTN Reviewed; 164 AA.
AC Q8A712;
DT 28-MAR-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid phosphatase {ECO:0000303|PubMed:18986982};
DE Short=KDN-9-P phosphatase {ECO:0000303|PubMed:18986982};
DE EC=3.1.3.103 {ECO:0000269|PubMed:18804026, ECO:0000269|PubMed:18986982, ECO:0000269|PubMed:23848398};
DE AltName: Full=2-keto-3-deoxy-D-glycero-D-galacto-nonic acid-9-phosphate phosphatase {ECO:0000303|PubMed:23848398};
DE Short=KDN9PP {ECO:0000303|PubMed:23848398};
DE AltName: Full=3-deoxy-D-glycero-D-galacto-nonulopyranosonate 9-phosphatase {ECO:0000305};
GN OrderedLocusNames=BT_1713 {ECO:0000312|EMBL:AAO76820.1};
OS Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 /
OS CCUG 10774 / NCTC 10582 / VPI-5482 / E50).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=226186;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=12663928; DOI=10.1126/science.1080029;
RA Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C.,
RA Hooper L.V., Gordon J.I.;
RT "A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.";
RL Science 299:2074-2076(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=19321416; DOI=10.1073/pnas.0901529106;
RA Mahowald M.A., Rey F.E., Seedorf H., Turnbaugh P.J., Fulton R.S.,
RA Wollam A., Shah N., Wang C., Magrini V., Wilson R.K., Cantarel B.L.,
RA Coutinho P.M., Henrissat B., Crock L.W., Russell A., Verberkmoes N.C.,
RA Hettich R.L., Gordon J.I.;
RT "Characterizing a model human gut microbiota composed of members of its two
RT dominant bacterial phyla.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:5859-5864(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBSTRATE
RP SPECIFICITY.
RX PubMed=18804026; DOI=10.1016/j.chembiol.2008.08.005;
RA Wang L., Lu Z., Allen K.N., Mariano P.S., Dunaway-Mariano D.;
RT "Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-
RT glycero-D-galacto-nononic acid (KDN).";
RL Chem. Biol. 15:893-897(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP MAGNESIUM IONS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, MUTAGENESIS OF THR-34; SER-37; GLU-56 AND ARG-64, COFACTOR,
RP SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=18986982; DOI=10.1074/jbc.m807056200;
RA Lu Z., Wang L., Dunaway-Mariano D., Allen K.N.;
RT "Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-
RT 9-phosphate phosphatase defines specificity elements in type C0
RT haloalkanoate dehalogenase family members.";
RL J. Biol. Chem. 284:1224-1233(2009).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF WILD-TYPE AND DOUBLE MUTANTS
RP ALA-56/ALA-67 IN COMPLEX WITH SUBSTRATE ANALOG AND MAGNESIUM IONS,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
RP GLU-56 AND LYS-67, COFACTOR, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=23848398; DOI=10.1021/bi400659k;
RA Daughtry K.D., Huang H., Malashkevich V., Patskovsky Y., Liu W.,
RA Ramagopal U., Sauder J.M., Burley S.K., Almo S.C., Dunaway-Mariano D.,
RA Allen K.N.;
RT "Structural basis for the divergence of substrate specificity and
RT biological function within HAD phosphatases in lipopolysaccharide and
RT sialic acid biosynthesis.";
RL Biochemistry 52:5372-5386(2013).
CC -!- FUNCTION: Involved in the biosynthesis of 2-keto-3-deoxy-D-glycero-D-
CC galacto-nononic acid used in cell-wall polysaccharides
CC (PubMed:18804026). Catalyzes the hydrolysis of 2-keto-3-deoxy-D-
CC glycero-D-galacto-9-phosphonononic acid (KDN-9-P) to yield 2-keto-3-
CC deoxy-D-glycero-D-galacto-nononic acid (KDN) (PubMed:18804026,
CC PubMed:18986982, PubMed:23848398). Also able to hydrolyze N-
CC acetylneuraminate-9-phosphate (Neu5NAc-9-P), 2-keto-3-deoxy-D-manno-
CC octulosonate-8-phosphate (KDO-8-P), phosphoenolpyruvate (PEP),
CC gluconate 6-phosphate, tyrosine phosphate ester and glucose-6-P as
CC substrate (PubMed:18804026, PubMed:18986982, PubMed:23848398).
CC {ECO:0000269|PubMed:18804026, ECO:0000269|PubMed:18986982,
CC ECO:0000269|PubMed:23848398}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate 9-
CC phosphate + H2O = 3-deoxy-D-glycero-beta-D-galacto-non-2-
CC ulopyranosonate + phosphate; Xref=Rhea:RHEA:49216, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:90987, ChEBI:CHEBI:90988;
CC EC=3.1.3.103; Evidence={ECO:0000269|PubMed:18804026,
CC ECO:0000269|PubMed:18986982, ECO:0000269|PubMed:23848398};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:18986982, ECO:0000269|PubMed:23848398};
CC Note=Binds 1 magnesium ion per subunit. {ECO:0000269|PubMed:18986982,
CC ECO:0000269|PubMed:23848398};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.3 uM for magnesium ion {ECO:0000269|PubMed:18986982};
CC KM=100 uM for 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic
CC acid (KDN-9-P) {ECO:0000269|PubMed:18986982};
CC KM=105 uM for 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic
CC acid (KDN-9-P) {ECO:0000269|PubMed:23848398};
CC KM=110 uM for 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic
CC acid (KDN-9-P) {ECO:0000269|PubMed:18804026};
CC KM=120 uM for N-acetylneuraminate-9-phosphate (Neu5NAc-9-P)
CC {ECO:0000269|PubMed:18804026};
CC KM=310 uM for 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-
CC P) {ECO:0000269|PubMed:18804026};
CC KM=430 uM for 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-
CC P) {ECO:0000269|PubMed:23848398};
CC Note=kcat is 72 min(-1) for 2-keto-3-deoxy-D-glycero-D-galacto-9-
CC phosphonononic acid (KDN-9-P) as substrate (PubMed:18804026). kcat is
CC 44 min(-1) for N-acetylneuraminate-9-phosphate (Neu5NAc-9-P) as
CC substrate (PubMed:18804026). kcat is 3.8 min(-1) for 2-keto-3-deoxy-
CC D-manno-octulosonate-8-phosphate (KDO-8-P) as substrate
CC (PubMed:18804026). kcat is 1.2 sec(-1) for 2-keto-3-deoxy-D-glycero-
CC D-galacto-9-phosphonononic acid (KDN-9-P) as substrate
CC (PubMed:18986982). {ECO:0000269|PubMed:18804026,
CC ECO:0000269|PubMed:18986982};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:18986982,
CC ECO:0000269|PubMed:23848398}.
CC -!- SIMILARITY: Belongs to the KdsC family. {ECO:0000305}.
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DR EMBL; AE015928; AAO76820.1; -; Genomic_DNA.
DR RefSeq; NP_810626.1; NC_004663.1.
DR RefSeq; WP_008767822.1; NZ_UYXG01000034.1.
DR PDB; 3E81; X-ray; 1.63 A; A/B/C/D=1-164.
DR PDB; 3E84; X-ray; 1.85 A; A/B/C/D=1-164.
DR PDB; 3E8M; X-ray; 1.10 A; A/B/C/D=1-164.
DR PDB; 4HGO; X-ray; 2.10 A; A/B/C/D=1-164.
DR PDB; 4HGQ; X-ray; 2.28 A; A/B/C/D/E/F/G/H=1-164.
DR PDB; 4HGR; X-ray; 2.05 A; A/B/C/D/E/F/G/H=1-164.
DR PDBsum; 3E81; -.
DR PDBsum; 3E84; -.
DR PDBsum; 3E8M; -.
DR PDBsum; 4HGO; -.
DR PDBsum; 4HGQ; -.
DR PDBsum; 4HGR; -.
DR AlphaFoldDB; Q8A712; -.
DR SMR; Q8A712; -.
DR STRING; 226186.BT_1713; -.
DR PaxDb; Q8A712; -.
DR PRIDE; Q8A712; -.
DR EnsemblBacteria; AAO76820; AAO76820; BT_1713.
DR GeneID; 60927701; -.
DR KEGG; bth:BT_1713; -.
DR PATRIC; fig|226186.12.peg.1756; -.
DR eggNOG; COG1778; Bacteria.
DR HOGENOM; CLU_106694_1_0_10; -.
DR InParanoid; Q8A712; -.
DR OMA; FDFHYHG; -.
DR BioCyc; MetaCyc:MON-14548; -.
DR BRENDA; 3.1.3.103; 709.
DR EvolutionaryTrace; Q8A712; -.
DR Proteomes; UP000001414; Chromosome.
DR GO; GO:0016788; F:hydrolase activity, acting on ester bonds; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006549; HAD-SF_hydro_IIIA.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR010023; KdsC_fam.
DR PIRSF; PIRSF006118; KDO8-P_Ptase; 1.
DR SFLD; SFLDG01138; C1.6.2:_Deoxy-d-mannose-octulo; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01662; HAD-SF-IIIA; 1.
DR TIGRFAMs; TIGR01670; KdsC-phosphatas; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..164
FT /note="2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic
FT acid phosphatase"
FT /id="PRO_0000443723"
FT BINDING 10
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18986982,
FT ECO:0000269|PubMed:23848398, ECO:0007744|PDB:3E84,
FT ECO:0007744|PDB:4HGO, ECO:0007744|PDB:4HGQ,
FT ECO:0007744|PDB:4HGR"
FT BINDING 12
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18986982,
FT ECO:0000269|PubMed:23848398, ECO:0007744|PDB:3E84,
FT ECO:0007744|PDB:4HGO, ECO:0007744|PDB:4HGQ,
FT ECO:0007744|PDB:4HGR"
FT BINDING 34
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18986982,
FT ECO:0000305|PubMed:23848398, ECO:0007744|PDB:3E81,
FT ECO:0007744|PDB:3E8M, ECO:0007744|PDB:4HGO"
FT BINDING 54..56
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18986982,
FT ECO:0000305|PubMed:23848398, ECO:0007744|PDB:3E81,
FT ECO:0007744|PDB:3E84, ECO:0007744|PDB:4HGO"
FT BINDING 64..67
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18986982,
FT ECO:0000305|PubMed:23848398, ECO:0007744|PDB:3E81,
FT ECO:0007744|PDB:3E8M, ECO:0007744|PDB:4HGO"
FT BINDING 80
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18986982,
FT ECO:0000305|PubMed:23848398, ECO:0007744|PDB:3E81,
FT ECO:0007744|PDB:3E84, ECO:0007744|PDB:4HGO"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18986982,
FT ECO:0000269|PubMed:23848398, ECO:0007744|PDB:3E84,
FT ECO:0007744|PDB:4HGO, ECO:0007744|PDB:4HGQ,
FT ECO:0007744|PDB:4HGR"
FT BINDING 106
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18986982,
FT ECO:0007744|PDB:3E81, ECO:0007744|PDB:3E84"
FT MUTAGEN 34
FT /note="T->A: 13-fold decrease of the catalytic efficiency
FT and 4-fold decrease of the affinity for 2-keto-3-deoxy-D-
FT glycero-D-galacto-9-phosphonononic acid (KDN-9-P)."
FT /evidence="ECO:0000269|PubMed:18986982"
FT MUTAGEN 37
FT /note="S->A: 2-fold decrease of the affinity for 2-keto-3-
FT deoxy-D-glycero-D-galacto-9-phosphonononic acid (KDN-9-P)."
FT /evidence="ECO:0000269|PubMed:18986982"
FT MUTAGEN 56
FT /note="E->A: Strong decrease of the catalytic efficiency
FT and 4-fold decrease of the affinity for 2-keto-3-deoxy-D-
FT glycero-D-galacto-9-phosphonononic acid (KDN-9-P). Displays
FT a 46-fold decrease in the catalytic efficiency and 25-fold
FT decrease of the affinity with 2-keto-3-deoxy-D-glycero-D-
FT galacto-9-phosphonononic acid (KDN-9-P) as substrate,
FT however with 2-keto-3-deoxy-D-manno-octulosonate-8-
FT phosphate (KDO-8-P) serving as substrate the catalytic
FT efficiency and affinity are almost unchanged. Displays a
FT 300-fold decrease of the catalytic efficiency and an
FT unchanged affinity with 2-keto-3-deoxy-D-glycero-D-galacto-
FT 9-phosphonononic acid (KDN-9-P) as substrate, however with
FT 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P)
FT serving as substrate the catalytic efficiency and affinity
FT are almost unchanged; when associated with A-67."
FT /evidence="ECO:0000269|PubMed:18986982,
FT ECO:0000269|PubMed:23848398"
FT MUTAGEN 64
FT /note="R->A: Loss of phosphatase activity."
FT /evidence="ECO:0000269|PubMed:18986982"
FT MUTAGEN 67
FT /note="K->A: Displays a 300-fold decrease of the catalytic
FT efficiency and an unchanged affinity with 2-keto-3-deoxy-D-
FT glycero-D-galacto-9-phosphonononic acid (KDN-9-P) as
FT substrate, however with 2-keto-3-deoxy-D-manno-
FT octulosonate-8-phosphate (KDO-8-P) serving as substrate the
FT catalytic efficiency and affinity are almost unchanged;
FT when associated with A-56."
FT /evidence="ECO:0000269|PubMed:18986982"
FT STRAND 6..9
FT /evidence="ECO:0007829|PDB:3E8M"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 15..22
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 37..45
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 80..91
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:3E8M"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 125..128
FT /evidence="ECO:0007829|PDB:3E8M"
FT TURN 139..142
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 143..151
FT /evidence="ECO:0007829|PDB:3E8M"
FT HELIX 156..162
FT /evidence="ECO:0007829|PDB:3E8M"
SQ SEQUENCE 164 AA; 18340 MW; 9E784096D5AC3C1B CRC64;
MKEIKLILTD IDGVWTDGGM FYDQTGNEWK KFNTSDSAGI FWAHNKGIPV GILTGEKTEI
VRRRAEKLKV DYLFQGVVDK LSAAEELCNE LGINLEQVAY IGDDLNDAKL LKRVGIAGVP
ASAPFYIRRL STIFLEKRGG EGVFREFVEK VLGINLEDFI AVIQ
