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Protein

Transcription elongation factor Spt4

Gene

spt4

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Stimulates transcription elongation.UniRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi6 – 61ZincUniRule annotation2 Publications
Metal bindingi9 – 91ZincUniRule annotation2 Publications
Metal bindingi18 – 181ZincUniRule annotation2 Publications
Metal bindingi21 – 211ZincUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription elongation factor Spt4UniRule annotation
Gene namesi
Name:spt4UniRule annotation
Ordered Locus Names:PF0255
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 6161Transcription elongation factor Spt4PRO_0000422131Add
BLAST

Interactioni

Subunit structurei

Heterodimer composed of Spt4 and Spt5.UniRule annotation2 Publications

Protein-protein interaction databases

DIPiDIP-59595N.
IntActiQ8U440. 1 interaction.
MINTiMINT-8173563.
STRINGi186497.PF0255.

Structurei

Secondary structure

1
61
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Turni7 – 93Combined sources
Beta strandi11 – 177Combined sources
Turni19 – 213Combined sources
Beta strandi26 – 283Combined sources
Beta strandi30 – 378Combined sources
Helixi39 – 413Combined sources
Helixi43 – 486Combined sources
Beta strandi54 – 607Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RYQX-ray1.38A2-61[»]
3P8BX-ray1.80A/C1-61[»]
3QQCX-ray3.30E1-61[»]
ProteinModelPortaliQ8U440.
SMRiQ8U440. Positions 3-61.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8U440.

Family & Domainsi

Domaini

Contains a N-terminal zinc-binding domain and a C-terminal NGN-binding domain.2 Publications

Sequence similaritiesi

Belongs to the archaeal Spt4 family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04077. Archaea.
COG2093. LUCA.
HOGENOMiHOG000229326.
KOiK03050.
OMAiRDLSDEW.

Family and domain databases

HAMAPiMF_00949. Spt4_arch.
InterProiIPR029040. RPABC4/Spt4.
IPR022800. Spt4/RpoE2_Znf.
IPR007178. Spt4_arch.
[Graphical view]
PfamiPF06093. Spt4. 1 hit.
[Graphical view]
ProDomiPD019197. DNA-dir_RNA_pol_RpoE2_arc. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM01389. Spt4. 1 hit.
[Graphical view]
SUPFAMiSSF63393. SSF63393. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8U440-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEKACRHCH YITSEDRCPV CGSRDLSEEW FDLVIIVDVE NSEIAKKIGA
60
KVPGKYAIRV R
Length:61
Mass (Da):6,953
Last modified:June 1, 2002 - v1
Checksum:iCA46E8DBF597B8ED
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL80379.1.
RefSeqiWP_011011370.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL80379; AAL80379; PF0255.
GeneIDi1468089.
KEGGipfu:PF0255.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL80379.1.
RefSeqiWP_011011370.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RYQX-ray1.38A2-61[»]
3P8BX-ray1.80A/C1-61[»]
3QQCX-ray3.30E1-61[»]
ProteinModelPortaliQ8U440.
SMRiQ8U440. Positions 3-61.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59595N.
IntActiQ8U440. 1 interaction.
MINTiMINT-8173563.
STRINGi186497.PF0255.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL80379; AAL80379; PF0255.
GeneIDi1468089.
KEGGipfu:PF0255.

Phylogenomic databases

eggNOGiarCOG04077. Archaea.
COG2093. LUCA.
HOGENOMiHOG000229326.
KOiK03050.
OMAiRDLSDEW.

Miscellaneous databases

EvolutionaryTraceiQ8U440.

Family and domain databases

HAMAPiMF_00949. Spt4_arch.
InterProiIPR029040. RPABC4/Spt4.
IPR022800. Spt4/RpoE2_Znf.
IPR007178. Spt4_arch.
[Graphical view]
PfamiPF06093. Spt4. 1 hit.
[Graphical view]
ProDomiPD019197. DNA-dir_RNA_pol_RpoE2_arc. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM01389. Spt4. 1 hit.
[Graphical view]
SUPFAMiSSF63393. SSF63393. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "Parameter-space screening: a powerful tool for high-throughput crystal structure determination."
    Liu Z.J., Lin D., Tempel W., Praissman J.L., Rose J.P., Wang B.C.
    Acta Crystallogr. D 61:520-527(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.38 ANGSTROMS) OF 2-61.
  3. "Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity."
    Martinez-Rucobo F.W., Sainsbury S., Cheung A.C., Cramer P.
    EMBO J. 30:1302-1310(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS) IN COMPLEX WITH SPT5; RNAP AND ZINC, FUNCTION, SUBUNIT, DOMAIN.
  4. "RNA polymerase and transcription elongation factor Spt4/5 complex structure."
    Klein B.J., Bose D., Baker K.J., Yusoff Z.M., Zhang X., Murakami K.S.
    Proc. Natl. Acad. Sci. U.S.A. 108:546-550(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH SPT5 AND ZINC, FUNCTION, SUBUNIT, DOMAIN.

Entry informationi

Entry nameiSPT4_PYRFU
AccessioniPrimary (citable) accession number: Q8U440
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2013
Last sequence update: June 1, 2002
Last modified: May 11, 2016
This is version 81 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, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.