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Protein

dTDP-glucose 4,6-dehydratase

Gene

rmlB

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction. Involved in the biosynthesis of the dTDP-L-rhamnose which is a component of the critical linker, D-N-acetylglucosamine-L-rhamnose disaccharide, which connects the galactan region of arabinogalactan to peptidoglycan via a phosphodiester linkage.1 Publication

Catalytic activityi

dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.

Cofactori

NAD+By similarityNote: Binds 1 NAD+ per subunit.By similarity

Pathwayi: dTDP-L-rhamnose biosynthesis

This protein is involved in the pathway dTDP-L-rhamnose biosynthesis, which is part of Carbohydrate biosynthesis.
View all proteins of this organism that are known to be involved in the pathway dTDP-L-rhamnose biosynthesis and in Carbohydrate biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei81 – 811Substrate; via carbonyl oxygenBy similarity
Binding sitei96 – 961NADBy similarity
Active sitei121 – 1211Proton donorBy similarity
Active sitei122 – 1221Proton acceptorBy similarity
Active sitei147 – 1471Proton acceptorBy similarity
Binding sitei176 – 1761SubstrateBy similarity
Binding sitei177 – 1771NAD; via amide nitrogenBy similarity
Binding sitei211 – 2111SubstrateBy similarity
Binding sitei246 – 2461SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi7 – 137NADSequence analysis
Nucleotide bindingi33 – 364NADBy similarity
Nucleotide bindingi57 – 582NADBy similarity
Nucleotide bindingi147 – 1515NADBy similarity

GO - Molecular functioni

  • dTDP-glucose 4,6-dehydratase activity Source: UniProtKB

GO - Biological processi

  • dTDP-rhamnose biosynthetic process Source: UniProtKB-UniPathway
  • extracellular polysaccharide biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-1512-MONOMER.
UniPathwayiUPA00124.

Names & Taxonomyi

Protein namesi
Recommended name:
dTDP-glucose 4,6-dehydratase (EC:4.2.1.46)
Gene namesi
Name:rmlB
Synonyms:rfbB
Ordered Locus Names:MSMEG_1512, MSMEI_1476
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 331331dTDP-glucose 4,6-dehydratasePRO_0000399898Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi246196.MSMEG_1512.

Structurei

3D structure databases

ProteinModelPortaliA0QSK6.
SMRiA0QSK6. Positions 3-326.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni120 – 1223Substrate bindingBy similarity
Regioni186 – 1872Substrate bindingBy similarity
Regioni202 – 2043Substrate bindingBy similarity
Regioni270 – 2734Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C1B. Bacteria.
COG1088. LUCA.
HOGENOMiHOG000168006.
KOiK01710.
OMAiKEWWTRI.
OrthoDBiEOG6PZXCX.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005888. dTDP_Gluc_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01181. dTDP_gluc_dehyt. 1 hit.

Sequencei

Sequence statusi: Complete.

A0QSK6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLLVTGGAG FIGANFVHLA LREARTSSIT VLDALTYAGS RESLAPVADR
60 70 80 90 100
IRLVQGDITD AALVGDLVAE SDAVVHFAAE THVDNALADP EPFLHSNVVG
110 120 130 140 150
TYTILEAVRR HNVRLHHVST DEVYGDLELD NPARFNETTP YNPSSPYSST
160 170 180 190 200
KAAADLLVRA WVRSYGVRAT ISNCSNNYGP YQHVEKFIPR QITNVLTGRR
210 220 230 240 250
PKLYGAGANV RDWIHVDDHN SAVWRILTDG TIGRTYLIGA ECERNNLTVM
260 270 280 290 300
RTILKLMGRD PDDFDHVTDR AGHDLRYAID PSTLQDELGW APKHTDFEAG
310 320 330
LTDTIDWYRA NESWWRPLKD TVEAKYQERG Q
Length:331
Mass (Da):36,967
Last modified:January 9, 2007 - v1
Checksum:i7DC0A0520677DDF0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK70086.1.
CP001663 Genomic DNA. Translation: AFP37949.1.
RefSeqiWP_003892900.1. NZ_CP009494.1.
YP_885894.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK70086; ABK70086; MSMEG_1512.
AFP37949; AFP37949; MSMEI_1476.
GeneIDi4531259.
KEGGimsb:LJ00_07555.
msg:MSMEI_1476.
msm:MSMEG_1512.
PATRICi18075481. VBIMycSme59918_1497.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK70086.1.
CP001663 Genomic DNA. Translation: AFP37949.1.
RefSeqiWP_003892900.1. NZ_CP009494.1.
YP_885894.1. NC_008596.1.

3D structure databases

ProteinModelPortaliA0QSK6.
SMRiA0QSK6. Positions 3-326.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_1512.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK70086; ABK70086; MSMEG_1512.
AFP37949; AFP37949; MSMEI_1476.
GeneIDi4531259.
KEGGimsb:LJ00_07555.
msg:MSMEI_1476.
msm:MSMEG_1512.
PATRICi18075481. VBIMycSme59918_1497.

Phylogenomic databases

eggNOGiENOG4105C1B. Bacteria.
COG1088. LUCA.
HOGENOMiHOG000168006.
KOiK01710.
OMAiKEWWTRI.
OrthoDBiEOG6PZXCX.

Enzyme and pathway databases

UniPathwayiUPA00124.
BioCyciMSME246196:GJ4Y-1512-MONOMER.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005888. dTDP_Gluc_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01181. dTDP_gluc_dehyt. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  2. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
    Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
    Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  3. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
    Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
    Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  4. "rmlB and rmlC genes are essential for growth of mycobacteria."
    Li W., Xin Y., McNeil M.R., Ma Y.
    Biochem. Biophys. Res. Commun. 342:170-178(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS.

Entry informationi

Entry nameiRMLB_MYCS2
AccessioniPrimary (citable) accession number: A0QSK6
Secondary accession number(s): I7G5T4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 2, 2010
Last sequence update: January 9, 2007
Last modified: December 9, 2015
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.