RNA polymerase sigma factor - Thermus thermophilus

Preferred order of sections

Names and origin

Protein names

Recommended name:
RNA polymerase sigma factor RuleBase RU000715

Gene names

Name:

sigA EMBL BAA74758.1

Organism

Thermus thermophilus EMBL BAA74758.1

Taxonomic identifier

274 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	423 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. RuleBase RU000715
Sequence similarities	Belongs to the sigma-70 factor family. RuleBase RU000715

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding SAAS SAAS007627 RuleBase RU000715 Magnesium PDB 1IW7 PDB 1SMY Metal-binding PDB 1IW7 PDB 1SMY
Molecular function	Sigma factor SAAS SAAS007627 RuleBase RU000715
Technical term	3D-structure PDB 1IW7 PDB 1SMY
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion 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 electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Sites

Metal binding

286

1

Magnesium 1 PDB 1SMY

Metal binding

287

1

Magnesium 1 PDB 1SMY

Metal binding

291

1

Magnesium 1; via amide nitrogen PDB 1SMY

Metal binding

409

1

Magnesium 2; via carbonyl oxygen PDB 1SMY

Metal binding

413

1

Magnesium 2 PDB 1SMY

Metal binding

416

1

Magnesium 2 PDB 1SMY

Sequences

Sequence

Length

Mass (Da)

Tools

Q9WX78 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 931A7B40B92CBC05
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FASTA

423

48,494

        10         20         30         40         50         60 
MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD LLDLPEEGEG 

        70         80         90        100        110        120 
LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV ELARKVEEGM EAIKKLSEIT 

       130        140        150        160        170        180 
GLDPDLIREV VRAKILGSAR VRHIPGLKET LDPKTVEEID QKLKSLPKEH KRYLHIAREG 

       190        200        210        220        230        240 
EAARQHLIEA NLRLVVSIAK KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT 

       250        260        270        280        290        300 
WWIRQAINRA IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD 

       310        320        330        340        350        360 
AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL SEELEKALSK 

       370        380        390        400        410        420 
LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI ENKALRKLKY HESRTRKLRD 


FLD

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References

[1]	"Cloning and characterization in Escherichia coli of the gene encoding the principal sigma factor of an extreme thermophile, Thermus thermophilus." Nishiyama M., Kobashi N., Tanaka K., Takahashi H., Tanokura M. FEMS Microbiol. Lett. 172:179-186(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: HB27 EMBL BAA74758.1.
[2]	"Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution." Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Nature 417:712-719(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS).
[3]	"Structural basis for transcription regulation by alarmone ppGpp." Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K., Yokoyama S., Vassylyev D.G. Cell 117:299-310(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH MAGNESIUM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB017014 Genomic DNA. Translation: BAA74758.1.

RefSeq

YP_004139.1. NC_005835.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IW7	X-ray	2.60	F/P	1-423	[»]
1SMY	X-ray	2.70	F/P	1-423	[»]

ProteinModelPortal

Q9WX78.

SMR

Q9WX78. Positions 74-423.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

2774849.

KEGG

tth:TTC0164.

PATRIC

23950721. VBITheThe54392_0165.

Phylogenomic databases

KO

K03086.

ProtClustDB

CLSK738324.

Family and domain databases

Gene3D

1.10.10.10. 2 hits.

InterPro

IPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR009042. RNA_pol_sigma70_r1_2.
IPR007627. RNA_pol_sigma70_r2.
IPR007624. RNA_pol_sigma70_r3.
IPR007630. RNA_pol_sigma70_r4.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]

PRINTS

PR00046. SIGMA70FCT.

SUPFAM

SSF88946. Sigma_r2. 1 hit.
SSF88659. Sigma_r3_r4. 2 hits.

TIGRFAMs

TIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.

PROSITE

PS00716. SIGMA70_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9WX78.

Entry information

Entry name

Q9WX78_THETH

Accession

Primary (citable) accession number: Q9WX78

Entry history

Integrated into UniProtKB/TrEMBL:	November 1, 1999
Last sequence update:	November 1, 1999
Last modified:	May 1, 2013
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)