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Protein

dTDP-4-dehydro-6-deoxyglucose 3-epimerase

Gene

chmJ

Organism
Streptomyces bikiniensis
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dTDP-4-oxo-6-deoxyglucose to dTDP-4-oxo-6-deoxyallose, via a C-3 epimerization. This is a step in the biosynthesis of the mycinose moiety of the chalcomycin antibiotic.1 Publication

Catalytic activityi

dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-allose.1 Publication

Kineticsi

kcat is 6.4 sec(-1).

  1. KM=04 mM for dTDP-4-dehydro-6-deoxy-alpha-D-glucose

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 211Substrate
Binding sitei26 – 261Substrate
Binding sitei45 – 451Substrate
Binding sitei57 – 571Substrate
Active sitei60 – 601Proton acceptor1 Publication
Binding sitei70 – 701Substrate
Binding sitei117 – 1171Substrate
Active sitei130 – 1301Proton donor1 Publication
Binding sitei136 – 1361Substrate
Binding sitei141 – 1411Substrate

GO - Molecular functioni

  1. dTDP-4-dehydrorhamnose 3,5-epimerase activity Source: InterPro

GO - Biological processi

  1. antibiotic biosynthetic process Source: UniProtKB-KW
  2. lipopolysaccharide biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Antibiotic biosynthesis, Carbohydrate metabolism

Names & Taxonomyi

Protein namesi
Recommended name:
dTDP-4-dehydro-6-deoxyglucose 3-epimerase (EC:5.1.3.27)
Alternative name(s):
dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase
dTDP-4-keto-6-deoxyglucose epimerase
dTDP-4-oxo-6-deoxy-D-glucose epimerase
Gene namesi
Name:chmJ
OrganismiStreptomyces bikiniensis
Taxonomic identifieri1896 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomyces

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi60 – 601H → N: No effect on substrate affinity, but 2400-fold reduction in activity. 1 Publication
Mutagenesisi130 – 1301Y → F: Slight decrease in substrate affinity, and 1650-fold reduction in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 196196dTDP-4-dehydro-6-deoxyglucose 3-epimerasePRO_0000425106Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1
196
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 124Combined sources
Beta strandi16 – 194Combined sources
Beta strandi22 – 298Combined sources
Helixi30 – 378Combined sources
Beta strandi45 – 517Combined sources
Beta strandi55 – 628Combined sources
Beta strandi64 – 663Combined sources
Beta strandi70 – 8415Combined sources
Turni91 – 944Combined sources
Beta strandi96 – 1027Combined sources
Turni103 – 1053Combined sources
Beta strandi108 – 1114Combined sources
Beta strandi116 – 1216Combined sources
Beta strandi126 – 1349Combined sources
Helixi138 – 1403Combined sources
Beta strandi141 – 1433Combined sources
Turni149 – 1513Combined sources
Helixi165 – 1684Combined sources
Helixi173 – 1786Combined sources
Helixi185 – 19612Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4HMZX-ray2.00A/B/C/D1-196[»]
4HN0X-ray2.20A/B/C/D1-196[»]
4HN1X-ray1.60A/B/C/D1-196[»]
ProteinModelPortaliQ5SFD1.
SMRiQ5SFD1. Positions 2-189.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
InterProiIPR000888. dTDP_sugar_isom.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR21047. PTHR21047. 1 hit.
PfamiPF00908. dTDP_sugar_isom. 1 hit.
[Graphical view]
ProDomiPD001462. dTDP_sugar_isom. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF51182. SSF51182. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5SFD1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHPLSIEGAW SQEPVIHSDH RGRSHEWFRG ESFRQAFGHD FPVAQVNVAV
60 70 80 90 100
SHRGALRGIH YTEIPPGQAK YSVCVRGAGL DVVVDVRIGS PTFGRWEIVP
110 120 130 140 150
MDAERNTAVY LTAGLGRAFL SLTDDATLVY LCSSGYAPAR EHSVNPLDPD
160 170 180 190
LGIAWPDDIE PLLSDRDENA PTLATAERLG LLPTYQAWQE QQQAQR
Length:196
Mass (Da):21,683
Last modified:December 21, 2004 - v1
Checksum:i26C8CD880701F1CA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY509120 Genomic DNA. Translation: AAS79451.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY509120 Genomic DNA. Translation: AAS79451.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4HMZX-ray2.00A/B/C/D1-196[»]
4HN0X-ray2.20A/B/C/D1-196[»]
4HN1X-ray1.60A/B/C/D1-196[»]
ProteinModelPortaliQ5SFD1.
SMRiQ5SFD1. Positions 2-189.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
InterProiIPR000888. dTDP_sugar_isom.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR21047. PTHR21047. 1 hit.
PfamiPF00908. dTDP_sugar_isom. 1 hit.
[Graphical view]
ProDomiPD001462. dTDP_sugar_isom. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF51182. SSF51182. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae."
    Ward S.L., Hu Z., Schirmer A., Reid R., Revill W.P., Reeves C.D., Petrakovsky O.V., Dong S.D., Katz L.
    Antimicrob. Agents Chemother. 48:4703-4712(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: NRRL 2737.
  2. "Structural and functional studies on a 3'-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose."
    Kubiak R.L., Phillips R.K., Zmudka M.W., Ahn M.R., Maka E.M., Pyeatt G.L., Roggensack S.J., Holden H.M.
    Biochemistry 51:9375-9383(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF APOENZYME; COMPLEX WITH DTDP-QUINOVOSE AND MUTANT ASN-60/PHE-130 IN COMPLEX WITH DTDP, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, ACTIVE SITES, MUTAGENESIS OF HIS-60 AND TYR-130.
    Strain: NRRL 2737.

Entry informationi

Entry nameiCHMJ_STRBI
AccessioniPrimary (citable) accession number: Q5SFD1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 22, 2014
Last sequence update: December 21, 2004
Last modified: November 26, 2014
This is version 31 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

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.