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   23-FEB-2022, entry version 129.
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}.
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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   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-MONOMER; -.
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   METAL           25
FT                   /note="Magnesium"
FT   METAL           27
FT                   /note="Magnesium; via carbonyl oxygen"
FT   METAL           232
FT                   /note="Magnesium"
FT   METAL           233
FT                   /note="Magnesium"
FT                   /evidence="ECO:0000250"
FT   BINDING         209
FT                   /note="Phosphate"
FT                   /evidence="ECO:0000250"
FT   BINDING         235
FT                   /note="Phosphate"
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
//