NTDB_BACSU
ID NTDB_BACSU Reviewed; 282 AA.
AC O07565; Q796S1;
DT 02-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Kanosamine-6-phosphate phosphatase;
DE EC=3.1.3.92;
GN Name=ntdB; Synonyms=yhjK; OrderedLocusNames=BSU10540;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9579061; DOI=10.1099/00221287-144-4-859;
RA Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H.,
RA Venema G., Bron S.;
RT "The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus
RT subtilis chromosome contains several dysfunctional genes, the glyB marker,
RT many genes encoding transporter proteins, and the ubiquitous hit gene.";
RL Microbiology 144:859-875(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SEQUENCE REVISION TO C-TERMINUS.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [4]
RP FUNCTION IN THE NEOTREHALOSADIAMINE BIOSYNTHESIS, AND INDUCTION.
RC STRAIN=168 / 61884;
RX PubMed=14612444; DOI=10.1074/jbc.m309925200;
RA Inaoka T., Takahashi K., Yada H., Yoshida M., Ochi K.;
RT "RNA polymerase mutation activates the production of a dormant antibiotic
RT 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus
RT subtilis.";
RL J. Biol. Chem. 279:3885-3892(2004).
RN [5]
RP INDUCTION.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=17056753; DOI=10.1128/jb.01478-06;
RA Inaoka T., Ochi K.;
RT "Glucose uptake pathway-specific regulation of synthesis of
RT neotrehalosadiamine, a novel autoinducer produced in Bacillus subtilis.";
RL J. Bacteriol. 189:65-75(2007).
RN [6]
RP FUNCTION IN THE KANOSAMINE BIOSYNTHESIS AND AS A PHOSPHATASE, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBSTRATE SPECIFICITY.
RX PubMed=23586652; DOI=10.1021/ja4010255;
RA Vetter N.D., Langill D.M., Anjum S., Boisvert-Martel J., Jagdhane R.C.,
RA Omene E., Zheng H., van Straaten K.E., Asiamah I., Krol E.S., Sanders D.A.,
RA Palmer D.R.;
RT "A previously unrecognized kanosamine biosynthesis pathway in Bacillus
RT subtilis.";
RL J. Am. Chem. Soc. 135:5970-5973(2013).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 1-281 IN COMPLEX WITH MAGNESIUM
RP ION, COFACTOR, AND SUBUNIT.
RG Midwest center for structural genomics (MCSG);
RT "Crystal structure of yhjk (haloacid dehalogenase-like hydrolase protein)
RT from Bacillus subtilis.";
RL Submitted (JUL-2011) to the PDB data bank.
CC -!- FUNCTION: Involved in the biosynthesis of kanosamine (3-amino-3-deoxy-
CC D-glucose), which is known to have antibiotic and antifungal
CC properties, and to be a precursor of the antibiotic neotrehalosadiamine
CC (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose (NTD)). Catalyzes the
CC dephosphorylation of kanosamine 6-phosphate to yield kanosamine. There
CC is a trace amount of activity using glucosamine-6-phosphate.
CC {ECO:0000269|PubMed:14612444, ECO:0000269|PubMed:23586652}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-kanosamine 6-phosphate + H2O = kanosamine + phosphate;
CC Xref=Rhea:RHEA:37555, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:72732, ChEBI:CHEBI:72748; EC=3.1.3.92;
CC Evidence={ECO:0000269|PubMed:23586652};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000269|Ref.7};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=101 uM for kanosamine 6-phosphate (at pH 7.5 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:23586652};
CC Note=kcat is 32 sec(-1) for dephosphorylation with kanosamine 6-
CC phosphate (at pH 7.5 and 25 degrees Celsius).;
CC -!- PATHWAY: Antibiotic biosynthesis; kanosamine biosynthesis.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|Ref.7}.
CC -!- INDUCTION: Induced by neotrehalosadiamine.
CC {ECO:0000269|PubMed:14612444, ECO:0000269|PubMed:17056753}.
CC -!- MISCELLANEOUS: The production of neotrehalosadiamine is dormant in the
CC wild-type strain. A mutation in the beta subunit of RNA polymerase
CC activates the production of the neotrehalosadiamine (PubMed:14612444).
CC {ECO:0000305|PubMed:14612444}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. Cof family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Y14081; CAA74473.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12894.2; -; Genomic_DNA.
DR PIR; B69834; B69834.
DR RefSeq; NP_388935.2; NC_000964.3.
DR RefSeq; WP_003244845.1; NZ_JNCM01000035.1.
DR PDB; 3GYG; X-ray; 2.45 A; A/B/C/D=1-282.
DR PDBsum; 3GYG; -.
DR AlphaFoldDB; O07565; -.
DR SMR; O07565; -.
DR STRING; 224308.BSU10540; -.
DR PaxDb; O07565; -.
DR PRIDE; O07565; -.
DR EnsemblBacteria; CAB12894; CAB12894; BSU_10540.
DR GeneID; 939323; -.
DR KEGG; bsu:BSU10540; -.
DR PATRIC; fig|224308.179.peg.1133; -.
DR eggNOG; COG0561; Bacteria.
DR InParanoid; O07565; -.
DR OMA; NRCNPLA; -.
DR BioCyc; BSUB:BSU10540-MON; -.
DR BioCyc; MetaCyc:BSU10540-MON; -.
DR BRENDA; 3.1.3.92; 658.
DR SABIO-RK; O07565; -.
DR UniPathway; UPA01036; -.
DR EvolutionaryTrace; O07565; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0016791; F:phosphatase activity; IDA:UniProtKB.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006379; HAD-SF_hydro_IIB.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR006380; SPP_N.
DR Pfam; PF05116; S6PP; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01484; HAD-SF-IIB; 1.
DR PROSITE; PS01229; COF_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..282
FT /note="Kanosamine-6-phosphate phosphatase"
FT /id="PRO_0000054419"
FT ACT_SITE 25
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 25
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 209
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 232
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 233
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT CONFLICT 282
FT /note="S -> FMRRK (in Ref. 1; CAA74473)"
FT /evidence="ECO:0000305"
FT HELIX 1..4
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 5..7
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 19..25
FT /evidence="ECO:0007829|PDB:3GYG"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 37..55
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 69..78
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:3GYG"
FT TURN 91..94
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 109..116
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 121..134
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 161..178
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 180..186
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 197..205
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 209..220
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 227..231
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 237..240
FT /evidence="ECO:0007829|PDB:3GYG"
FT STRAND 243..248
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 254..259
FT /evidence="ECO:0007829|PDB:3GYG"
FT HELIX 268..279
FT /evidence="ECO:0007829|PDB:3GYG"
SQ SEQUENCE 282 AA; 32568 MW; 1673D38EBD4B8588 CRC64;
MLLSKKSEYK TLSTVEHPQY IVFCDFDETY FPHTIDEQKQ QDIYELEDYL EQKSKDGELI
IGWVTGSSIE SILDKMGRGK FRYFPHFIAS DLGTEITYFS EHNFGQQDNK WNSRINEGFS
KEKVEKLVKQ LHENHNILLN PQTQLGKSRY KHNFYYQEQD EINDKKNLLA IEKICEEYGV
SVNINRCNPL AGDPEDSYDV DFIPIGTGKN EIVTFMLEKY NLNTERAIAF GDSGNDVRML
QTVGNGYLLK NATQEAKNLH NLITDSEYSK GITNTLKKLI GS
