P66811 (RPSD_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase sigma-D factor

Gene names

Name:	sigD
Ordered Locus Names:	Rv3414c, MT3523
ORF Names:	MTCY78.15

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	212 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released By similarity. Ref.3
Induction	Positively autoregulates, probably directly, expressed at a relatively high level throughout exponential growth and during stationary phase. Expression decreases during O2 depletion (hypoxia). Ref.3
Disruption phenotype	Not essential for growth in culture. Upon disruption about 260 genes show significantly decreased expression while about 200 showed increased expression. BALB/c mice infected with the disruption mutant showed a moderate but significant decrease in virulence, surviving about 30% longer than wild-type. Ref.3
Sequence similarities	Belongs to the sigma-70 factor family. ECF subfamily.
Sequence caution	The sequence AAK47861.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Sigma factor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro pathogenesis Inferred from mutant phenotype PubMed 15659067. Source: MTBBASE regulation of fatty acid metabolic process Inferred from direct assay PubMed 19228590. Source: MTBBASE regulation of protein secretion Inferred from direct assay PubMed 19228590. Source: MTBBASE response to heat Inferred from expression pattern PubMed 10027986. Source: MTBBASE
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro sigma factor activity Inferred from mutant phenotype PubMed 15659067. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 212

212

RNA polymerase sigma-D factor

PRO_0000094023

Regions

DNA binding

176 – 195

20

H-T-H motif By similarity

Motif

75 – 88

14

Polymerase core binding Potential

Secondary structure

1

.

.

.

.

.

.

.

.

.

212

Helix Strand Turn

Details...

Helix

147 – 155

9

Helix

160 – 170

11

Helix

176 – 183

8

Helix

187 – 206

20

Sequences

	Sequence		Length	Mass (Da)
	P66811 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 12A157F6F66BB0C3	FASTA	212	22,919
	10 20 30 40 50 60 MVDPGVSPGC VRFVTLEISP SMTMQGERLD AVVAEAVAGD RNALREVLET IRPIVVRYCR 70 80 90 100 110 120 ARVGTVERSG LSADDVAQEV CLATITALPR YRDRGRPFLA FLYGIAAHKV ADAHRAAGRD 130 140 150 160 170 180 RAYPAETLPE RWSADAGPEQ MAIEADSVTR MNELLEILPA KQREILILRV VVGLSAEETA 190 200 210 AAVGSTTGAV RVAQHRALQR LKDEIVAAGD YA

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. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [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. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence." Raman S., Hazra R., Dascher C.C., Husson R.N. J. Bacteriol. 186:6605-6616(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000516 Genomic DNA. Translation: AAK47861.1. Different initiation.
AL123456 Genomic DNA. Translation: CCP46236.1.

PIR

C70737.

RefSeq

NP_217931.1. NC_000962.3.
NP_338047.1. NC_002755.2.
YP_006516900.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3VEP	X-ray	2.50	A/D/E/H	141-212	[»]
3VFZ	X-ray	1.90	A/B	141-212	[»]

ProteinModelPortal

P66811.

ModBase

Search...

Protein-protein interaction databases

STRING

83332.Rv3414c.

Proteomic databases

PRIDE

P66811.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK47861; AAK47861; MT3523.

GeneID

13317018.
887594.
923111.

KEGG

mtc:MT3523.
mtu:Rv3414c.

PATRIC

18129483. VBIMycTub22151_3837.

Organism-specific databases

TubercuList

Rv3414c.

Phylogenomic databases

eggNOG

COG1595.

HOGENOM

HOG000094755.

KO

K03088.

OMA

YARARIG.

ProtClustDB

PRK09648.

Family and domain databases

Gene3D

1.10.10.10. 1 hit.

InterPro

IPR014284. RNA_pol_sigma-70_dom.
IPR000838. RNA_pol_sigma70_ECF_CS.
IPR007627. RNA_pol_sigma70_r2.
IPR013249. RNA_pol_sigma70_r4_t2.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF04542. Sigma70_r2. 1 hit.
PF08281. Sigma70_r4_2. 1 hit.
[Graphical view]

SUPFAM

SSF88946. Sigma_r2. 1 hit.
SSF88659. Sigma_r3_r4. 1 hit.

TIGRFAMs

TIGR02937. sigma70-ECF. 1 hit.

PROSITE

PS01063. SIGMA70_ECF. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RPSD_MYCTU

Accession

Primary (citable) accession number: P66811
Secondary accession number(s): L0TFB3, Q50712

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 29, 2013
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program