NTDA_BACSU
ID NTDA_BACSU Reviewed; 441 AA.
AC O07566; Q796S0;
DT 02-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=3-oxo-glucose-6-phosphate:glutamate aminotransferase;
DE EC=2.6.1.104;
DE AltName: Full=3-dehydro-glucose-6-phosphate--glutamate transaminase;
DE AltName: Full=Kanosamine 6-phosphate transaminase;
GN Name=ntdA; Synonyms=yhjL; OrderedLocusNames=BSU10550;
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 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 [4]
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 [5]
RP FUNCTION IN THE KANOSAMINE BIOSYNTHESIS AND AS AN AMINOTRANSFERASE,
RP CATALYTIC ACTIVITY, 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 [6]
RP X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP AND SUBSTRATE, FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=24097983; DOI=10.1074/jbc.m113.500637;
RA van Straaten K.E., Ko J.B., Jagdhane R., Anjum S., Palmer D.R.,
RA Sanders D.A.;
RT "The structure of NtdA, a sugar aminotransferase involved in the kanosamine
RT biosynthetic pathway in Bacillus subtilis, reveals a new subclass of
RT aminotransferases.";
RL J. Biol. Chem. 288:34121-34130(2013).
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 reversible pyridoxal phosphate-dependent transamination of 3-dehydro-
CC alpha-D-glucose 6-phosphate to form alpha-D-kanosamine-6-phosphate. It
CC can only use alpha-anomer and glutamate is the only amino donor.
CC {ECO:0000269|PubMed:14612444, ECO:0000269|PubMed:23586652,
CC ECO:0000269|PubMed:24097983}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-dehydro-D-glucose 6-phosphate + L-glutamate = 2-oxoglutarate
CC + D-kanosamine 6-phosphate; Xref=Rhea:RHEA:37551, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:72748, ChEBI:CHEBI:75052;
CC EC=2.6.1.104; Evidence={ECO:0000269|PubMed:23586652};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:24097983};
CC -!- PATHWAY: Antibiotic biosynthesis; kanosamine biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24097983}.
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 DegT/DnrJ/EryC1 family. {ECO:0000305}.
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DR EMBL; Y14081; CAA74474.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12895.1; -; Genomic_DNA.
DR PIR; C69834; C69834.
DR RefSeq; NP_388936.1; NC_000964.3.
DR RefSeq; WP_003245503.1; NZ_JNCM01000035.1.
DR PDB; 4K2B; X-ray; 2.31 A; A/B=1-441.
DR PDB; 4K2I; X-ray; 2.22 A; A/B=1-441.
DR PDB; 4K2M; X-ray; 1.71 A; A/B=1-441.
DR PDBsum; 4K2B; -.
DR PDBsum; 4K2I; -.
DR PDBsum; 4K2M; -.
DR AlphaFoldDB; O07566; -.
DR SMR; O07566; -.
DR STRING; 224308.BSU10550; -.
DR PaxDb; O07566; -.
DR PRIDE; O07566; -.
DR EnsemblBacteria; CAB12895; CAB12895; BSU_10550.
DR GeneID; 939788; -.
DR KEGG; bsu:BSU10550; -.
DR PATRIC; fig|224308.179.peg.1134; -.
DR eggNOG; COG0399; Bacteria.
DR InParanoid; O07566; -.
DR OMA; GLERMKY; -.
DR PhylomeDB; O07566; -.
DR BioCyc; BSUB:BSU10550-MON; -.
DR BioCyc; MetaCyc:BSU10550-MON; -.
DR BRENDA; 2.6.1.104; 658.
DR UniPathway; UPA01036; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:UniProtKB.
DR GO; GO:0008483; F:transaminase activity; IDA:UniProtKB.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IDA:UniProtKB.
DR GO; GO:0000271; P:polysaccharide biosynthetic process; IBA:GO_Central.
DR CDD; cd00616; AHBA_syn; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000653; DegT/StrS_aminotransferase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR30244; PTHR30244; 1.
DR Pfam; PF01041; DegT_DnrJ_EryC1; 1.
DR PIRSF; PIRSF000390; PLP_StrS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminotransferase; Antibiotic biosynthesis;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..441
FT /note="3-oxo-glucose-6-phosphate:glutamate
FT aminotransferase"
FT /id="PRO_0000110006"
FT BINDING 98..99
FT /ligand="substrate"
FT BINDING 125..126
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT BINDING 151
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 225
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 242
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 244..246
FT /ligand="substrate"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 282
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 292
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:24097983"
FT BINDING 379
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24097983"
FT MOD_RES 247
FT /note="N6-(pyridoxal phosphate)lysine"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 11..22
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 36..38
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 39..44
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 78..91
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 101..114
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 125..135
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 153..161
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:4K2M"
FT TURN 172..174
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 205..215
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:4K2M"
FT TURN 230..235
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 256..261
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 263..273
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 285..288
FT /evidence="ECO:0007829|PDB:4K2I"
FT HELIX 297..306
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 310..327
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 329..333
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 344..346
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 349..354
FT /evidence="ECO:0007829|PDB:4K2M"
FT TURN 357..359
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 360..371
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 383..385
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 389..394
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 401..409
FT /evidence="ECO:0007829|PDB:4K2M"
FT STRAND 410..413
FT /evidence="ECO:0007829|PDB:4K2M"
FT HELIX 421..439
FT /evidence="ECO:0007829|PDB:4K2M"
SQ SEQUENCE 441 AA; 50141 MW; D2181BD4AFB20DA5 CRC64;
MQKQVKISGK SKENMSLLKH LKGDVQGKEL VIEDSIVNER WKQVLKEKID IEHDLFNYQK
NREISKVPFL PVDRLITNDE VEDILNTLTE VLPTGKFTSG PYLEQFEKVL STYLHKRYVI
ATSSGTDAIM IGLLALGLNP GDEVIMPANS FSATENAVLA SGGVPIYVDI NPQTFCIDPD
KIEEAITPYT KFILPVHLYG KHSDMQHIRQ IANRYKLKVI EDACQGIGLT DLGKYADITT
LSFNPYKNFG VCGKAGAIAT DNEELAKKCI QFSYHGFEVN VKNKKVINFG FNSKMDNLQA
AIGLERMKYL SLNNFKRLFL ADRYITQLAE LQNKGYIELP ELSEDHVWHL FPIKVRTEDR
ADIMTKLNED FGVQTDVYYP ILSHMQKTPL VQDKYAGLQL VHTEKAHSQV LHLPLYPSFT
LEEQDRVMEG LFHVIKQEIG V
