dTDP-4-dehydrorhamnose 3,5-epimerase - Mycobacterium tuberculosis

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O06330 (RMLC_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 77. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
dTDP-4-dehydrorhamnose 3,5-epimerase
EC=5.1.3.13

Alternative name(s):
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
dTDP-4-keto-6-deoxyglucose 3,5-epimerase
dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
dTDP-L-rhamnose synthase

Gene names

Name:	rmlC
Synonyms:	strM
Ordered Locus Names:	Rv3465, MT3571

Organism

Mycobacterium tuberculosis

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	202 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. 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. Ref.3
Catalytic activity	dTDP-4-dehydro-6-deoxy-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose. Ref.3
Pathway	Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.
Subunit structure	Homodimer. Ref.5 Ref.6
Miscellaneous	Was identified as a high-confidence drug target.
Sequence similarities	Belongs to the dTDP-4-dehydrorhamnose 3,5-epimerase family.

Ontologies

Keywords
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	dTDP-rhamnose biosynthetic process Inferred from direct assay. Source: MTBBASE extracellular polysaccharide biosynthetic process Inferred from genetic interaction Ref.3. Source: UniProtKB growth Inferred from direct assay Ref.3. Source: MTBBASE lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: InterPro
Molecular function	dTDP-4-dehydrorhamnose 3,5-epimerase activity Inferred from genetic interaction Ref.3. Source: UniProtKB protein homodimerization activity Inferred from physical interaction Ref.6. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 202

202

dTDP-4-dehydrorhamnose 3,5-epimerase

PRO_0000395349

Sites

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

Substrate

Binding site

119

Substrate

Binding site

171

Substrate

Secondary structure

202

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O06330 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: A6A1AFA0FC0F5871
Show »

FASTA

202

22,314

        10         20         30         40         50         60 
MKARELDVPG AWEITPTIHV DSRGLFFEWL TDHGFRAFAG HSLDVRQVNC SVSSAGVLRG 

        70         80         90        100        110        120 
LHFAQLPPSQ AKYVTCVSGS VFDVVVDIRE GSPTFGRWDS VLLDDQDRRT IYVSEGLAHG 

       130        140        150        160        170        180 
FLALQDNSTV MYLCSAEYNP QREHTICATD PTLAVDWPLV DGAAPSLSDR DAAAPSFEDV 

       190        200 
RASGLLPRWE QTQRFIGEMR GT

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. Barrell B.G. Nature 393:537-544(1998) [PubMed: 9634230] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed: 12218036] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"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: 16472764] [Abstract] Cited for: FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY.
[4]	"targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis." Raman K., Yeturu K., Chandra N. BMC Syst. Biol. 2:109-109(2008) [PubMed: 19099550] [Abstract] Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
[5]	"Novel inhibitors of an emerging target in Mycobacterium tuberculosis; substituted thiazolidinones as inhibitors of dTDP-rhamnose synthesis." Babaoglu K., Page M.A., Jones V.C., McNeil M.R., Dong C., Naismith J.H., Lee R.E. Bioorg. Med. Chem. Lett. 13:3227-3230(2003) [PubMed: 12951098] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
[6]	"Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway." Kantardjieff K.A., Kim C.Y., Naranjo C., Waldo G.S., Lekin T., Segelke B.W., Zemla A., Park M.S., Terwilliger T.C., Rupp B. Acta Crystallogr. D 60:895-902(2004) [PubMed: 15103135] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), SUBUNIT.
[7]	"RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation." Dong C., Major L.L., Srikannathasan V., Errey J.C., Giraud M.F., Lam J.S., Graninger M., Messner P., McNeil M.R., Field R.A., Whitfield C., Naismith J.H. J. Mol. Biol. 365:146-159(2007) [PubMed: 17046787] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, REACTION MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842583 Genomic DNA. Translation: CAB08731.1.
AE000516 Genomic DNA. Translation: AAK47911.1.

PIR

F70566.

RefSeq

NP_217982.1. NC_000962.2.
NP_338097.1. NC_002755.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1PM7	X-ray	2.20	A/B	1-202	[»]
1UPI	X-ray	1.70	A	1-202	[»]
2IXC	X-ray	1.79	A/B/C/D	1-202	[»]

ProteinModelPortal

O06330.

SMR

O06330. Positions 1-199.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBMYCT00000003973; EBMYCP00000003973; EBMYCG00000003971.
EBMYCT00000071036; EBMYCP00000069095; EBMYCG00000071031.

GeneID

887352.
922950.

GenomeReviews

Gene locus MT3571 in contig AE000516_GR.
Gene locus Rv3465 in contig AL123456_GR.

KEGG

mtc:MT3571.
mtu:Rv3465.

PATRIC

18129581. VBIMycTub22151_3886.

TIGR

MT3571.

Organism-specific databases

TubercuList

Rv3465.

Phylogenomic databases

GeneTree

EBGT00050000015200.

HOGENOM

HBG730537.

OMA

AWEITPR.

PhylomeDB

O06330.

ProtClustDB

CLSK792509.

Family and domain databases

InterPro

IPR011051. Cupin_RmlC_type.
IPR000888. dTDP_sugar_isom.
IPR014710. RmlC-like_jellyroll.
[Graphical view]

Gene3D

G3DSA:2.60.120.10. RmlC-like_jellyroll. 1 hit.

K01790.

PANTHER

PTHR21047. dTDP_sugar_isom. 1 hit.

Pfam

PF00908. dTDP_sugar_isom. 1 hit.
[Graphical view]

ProDom

PD001462. dTDP_sugar_isom. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF51182. RmlC_like_cupin. 1 hit.

TIGRFAMs

TIGR01221. RmlC. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RMLC_MYCTU

Accession

Primary (citable) accession number: O06330
Secondary accession number(s): Q7D5I3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 13, 2010
Last sequence update:	July 1, 1997
Last modified:	January 25, 2012
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents