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Protein

3-oxo-glucose-6-phosphate:glutamate aminotransferase

Gene

ntdA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of kanosamine (3-amino-3-deoxy-D-glucose), which is known to have antibiotic and antifungal properties, and to be a precursor of the antibiotic neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose (NTD)). Catalyzes the reversible pyridoxal phosphate-dependent transamination of 3-dehydro-alpha-D-glucose 6-phosphate to form alpha-D-kanosamine-6-phosphate. It can only use alpha-anomer and glutamate is the only amino donor.3 Publications

Catalytic activityi

Kanosamine 6-phosphate + 2-oxoglutarate = 3-dehydro-D-glucose 6-phosphate + L-glutamate.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Pathwayi: kanosamine biosynthesis

This protein is involved in the pathway kanosamine biosynthesis, which is part of Antibiotic biosynthesis.
View all proteins of this organism that are known to be involved in the pathway kanosamine biosynthesis and in Antibiotic biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei151 – 1511Substrate1 Publication
Binding sitei225 – 2251Pyridoxal phosphate1 Publication
Binding sitei242 – 2421Pyridoxal phosphate1 Publication
Binding sitei274 – 2741Substrate1 Publication
Binding sitei282 – 2821Substrate1 Publication
Binding sitei292 – 2921Pyridoxal phosphate1 Publication
Binding sitei379 – 3791Substrate1 Publication

GO - Molecular functioni

  • pyridoxal phosphate binding Source: UniProtKB
  • transaminase activity Source: UniProtKB

GO - Biological processi

  • antibiotic biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Aminotransferase, Transferase

Keywords - Biological processi

Antibiotic biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciBSUB:BSU10550-MONOMER.
MetaCyc:BSU10550-MONOMER.
BRENDAi2.6.1.104. 658.
UniPathwayiUPA01036.

Names & Taxonomyi

Protein namesi
Recommended name:
3-oxo-glucose-6-phosphate:glutamate aminotransferase (EC:2.6.1.104)
Alternative name(s):
3-dehydro-glucose-6-phosphate--glutamate transaminase
Kanosamine 6-phosphate transaminase
Gene namesi
Name:ntdA
Synonyms:yhjL
Ordered Locus Names:BSU10550
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4414413-oxo-glucose-6-phosphate:glutamate aminotransferasePRO_0000110006Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei247 – 2471N6-(pyridoxal phosphate)lysine

Proteomic databases

PaxDbiO07566.

Expressioni

Inductioni

Induced by neotrehalosadiamine.2 Publications

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005841.

Structurei

Secondary structure

1
441
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 73Combined sources
Helixi11 – 2212Combined sources
Beta strandi30 – 323Combined sources
Helixi36 – 383Combined sources
Helixi39 – 446Combined sources
Helixi51 – 544Combined sources
Helixi72 – 754Combined sources
Helixi78 – 9114Combined sources
Helixi92 – 943Combined sources
Beta strandi97 – 1004Combined sources
Helixi101 – 11414Combined sources
Beta strandi117 – 1237Combined sources
Helixi125 – 13511Combined sources
Beta strandi143 – 1464Combined sources
Beta strandi148 – 1503Combined sources
Helixi153 – 1619Combined sources
Beta strandi164 – 1674Combined sources
Turni172 – 1743Combined sources
Helixi179 – 1813Combined sources
Helixi183 – 1853Combined sources
Beta strandi190 – 1934Combined sources
Helixi198 – 2003Combined sources
Helixi205 – 21511Combined sources
Beta strandi218 – 2225Combined sources
Turni230 – 2356Combined sources
Beta strandi237 – 2426Combined sources
Beta strandi247 – 2493Combined sources
Beta strandi256 – 2616Combined sources
Helixi263 – 27311Combined sources
Beta strandi285 – 2884Combined sources
Helixi297 – 30610Combined sources
Helixi307 – 3093Combined sources
Helixi310 – 32718Combined sources
Helixi329 – 3335Combined sources
Beta strandi344 – 3463Combined sources
Beta strandi349 – 3546Combined sources
Turni357 – 3593Combined sources
Helixi360 – 37112Combined sources
Helixi383 – 3853Combined sources
Helixi389 – 3946Combined sources
Helixi401 – 4099Combined sources
Beta strandi410 – 4134Combined sources
Helixi421 – 43919Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4K2BX-ray2.31A/B1-441[»]
4K2IX-ray2.22A/B1-441[»]
4K2MX-ray1.71A/B1-441[»]
ProteinModelPortaliO07566.
SMRiO07566. Positions 66-434.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni98 – 992Substrate binding
Regioni125 – 1262Pyridoxal phosphate binding
Regioni244 – 2463Substrate binding

Sequence similaritiesi

Belongs to the DegT/DnrJ/EryC1 family.Curated

Phylogenomic databases

eggNOGiCOG0399. LUCA.
HOGENOMiHOG000230164.
InParanoidiO07566.
KOiK18653.
OMAiGVNTIIY.
OrthoDBiEOG6FNHJG.
PhylomeDBiO07566.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR000653. DegT/StrS_aminotransferase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF01041. DegT_DnrJ_EryC1. 1 hit.
[Graphical view]
PIRSFiPIRSF000390. PLP_StrS. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.

Sequencei

Sequence statusi: Complete.

O07566-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQKQVKISGK SKENMSLLKH LKGDVQGKEL VIEDSIVNER WKQVLKEKID
60 70 80 90 100
IEHDLFNYQK NREISKVPFL PVDRLITNDE VEDILNTLTE VLPTGKFTSG
110 120 130 140 150
PYLEQFEKVL STYLHKRYVI ATSSGTDAIM IGLLALGLNP GDEVIMPANS
160 170 180 190 200
FSATENAVLA SGGVPIYVDI NPQTFCIDPD KIEEAITPYT KFILPVHLYG
210 220 230 240 250
KHSDMQHIRQ IANRYKLKVI EDACQGIGLT DLGKYADITT LSFNPYKNFG
260 270 280 290 300
VCGKAGAIAT DNEELAKKCI QFSYHGFEVN VKNKKVINFG FNSKMDNLQA
310 320 330 340 350
AIGLERMKYL SLNNFKRLFL ADRYITQLAE LQNKGYIELP ELSEDHVWHL
360 370 380 390 400
FPIKVRTEDR ADIMTKLNED FGVQTDVYYP ILSHMQKTPL VQDKYAGLQL
410 420 430 440
VHTEKAHSQV LHLPLYPSFT LEEQDRVMEG LFHVIKQEIG V
Length:441
Mass (Da):50,141
Last modified:July 1, 1997 - v1
Checksum:iD2181BD4AFB20DA5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14081 Genomic DNA. Translation: CAA74474.1.
AL009126 Genomic DNA. Translation: CAB12895.1.
PIRiC69834.
RefSeqiNP_388936.1. NC_000964.3.
WP_003245503.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB12895; CAB12895; BSU10550.
GeneIDi939788.
KEGGibsu:BSU10550.
PATRICi18973812. VBIBacSub10457_1100.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14081 Genomic DNA. Translation: CAA74474.1.
AL009126 Genomic DNA. Translation: CAB12895.1.
PIRiC69834.
RefSeqiNP_388936.1. NC_000964.3.
WP_003245503.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4K2BX-ray2.31A/B1-441[»]
4K2IX-ray2.22A/B1-441[»]
4K2MX-ray1.71A/B1-441[»]
ProteinModelPortaliO07566.
SMRiO07566. Positions 66-434.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005841.

Proteomic databases

PaxDbiO07566.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12895; CAB12895; BSU10550.
GeneIDi939788.
KEGGibsu:BSU10550.
PATRICi18973812. VBIBacSub10457_1100.

Phylogenomic databases

eggNOGiCOG0399. LUCA.
HOGENOMiHOG000230164.
InParanoidiO07566.
KOiK18653.
OMAiGVNTIIY.
OrthoDBiEOG6FNHJG.
PhylomeDBiO07566.

Enzyme and pathway databases

UniPathwayiUPA01036.
BioCyciBSUB:BSU10550-MONOMER.
MetaCyc:BSU10550-MONOMER.
BRENDAi2.6.1.104. 658.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR000653. DegT/StrS_aminotransferase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF01041. DegT_DnrJ_EryC1. 1 hit.
[Graphical view]
PIRSFiPIRSF000390. PLP_StrS. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus subtilis chromosome contains several dysfunctional genes, the glyB marker, many genes encoding transporter proteins, and the ubiquitous hit gene."
    Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H., Venema G., Bron S.
    Microbiology 144:859-875(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "RNA polymerase mutation activates the production of a dormant antibiotic 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus subtilis."
    Inaoka T., Takahashi K., Yada H., Yoshida M., Ochi K.
    J. Biol. Chem. 279:3885-3892(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN THE NEOTREHALOSADIAMINE BIOSYNTHESIS, INDUCTION.
    Strain: 168 / 61884.
  4. "Glucose uptake pathway-specific regulation of synthesis of neotrehalosadiamine, a novel autoinducer produced in Bacillus subtilis."
    Inaoka T., Ochi K.
    J. Bacteriol. 189:65-75(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  5. Cited for: FUNCTION IN THE KANOSAMINE BIOSYNTHESIS AND AS AN AMINOTRANSFERASE, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
  6. "The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases."
    van Straaten K.E., Ko J.B., Jagdhane R., Anjum S., Palmer D.R., Sanders D.A.
    J. Biol. Chem. 288:34121-34130(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND SUBSTRATE, FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, SUBUNIT.
    Strain: 168.

Entry informationi

Entry nameiNTDA_BACSU
AccessioniPrimary (citable) accession number: O07566
Secondary accession number(s): Q796S0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2005
Last sequence update: July 1, 1997
Last modified: February 17, 2016
This is version 91 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The production of neotrehalosadiamine is dormant in the wild-type strain. A mutation in the beta subunit of RNA polymerase activates the production of the neotrehalosadiamine (PubMed:14612444).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.