DNA-directed RNA polymerase II subunit RPB4

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O15514 (RPB4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 124. History...

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

Documents (4) |

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:
DNA-directed RNA polymerase II subunit RPB4
Short name=RNA polymerase II subunit B4

Alternative name(s):
DNA-directed RNA polymerase II subunit D
RNA polymerase II 16 kDa subunit
Short name=RPB16

Gene names

Name:

POLR2D

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	142 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA By similarity. Ref.3
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex. Ref.3
Subcellular location	Nucleus Ref.3.
Sequence similarities	Belongs to the eukaryotic RPB4 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	7-methylguanosine mRNA capping Traceable author statement. Source: Reactome mRNA splicing, via spliceosome Traceable author statement. Source: Reactome positive regulation of viral transcription Traceable author statement. Source: Reactome protein phosphorylation Inferred from direct assay Ref.3. Source: GOC transcription elongation from RNA polymerase II promoter Traceable author statement. Source: Reactome transcription initiation from RNA polymerase II promoter Traceable author statement. Source: Reactome transcription-coupled nucleotide-excision repair Traceable author statement. Source: Reactome viral reproduction Traceable author statement. Source: Reactome
Cellular_component	DNA-directed RNA polymerase II, core complex Inferred from direct assay Ref.1 Ref.3. Source: UniProtKB
Molecular_function	DNA-directed RNA polymerase activity Inferred from mutant phenotype Ref.1. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 142

142

DNA-directed RNA polymerase II subunit RPB4

PRO_0000073981

Secondary structure

142

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O15514 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: 8A670386C433BE93
Show »

FASTA

142

16,311

        10         20         30         40         50         60 
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV 

        70         80         90        100        110        120 
FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL ANLCPETAEE SKALIPSLEG 

       130        140 
RFEDEELQQI LDDIQTKRSF QY

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II." Khazak V., Estojak J., Cho H., Majors J.A., Sonoda G., Testa J.R., Golemis E.A. Mol. Cell. Biol. 18:1935-1945(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]. Tissue: Cervix carcinoma.
[2]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung and Skin.
[3]	"Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes." Kershnar E., Wu S.-Y., Chiang C.-M. J. Biol. Chem. 273:34444-34453(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II CORE-COMPLEX, SUBCELLULAR LOCATION.
[4]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[5]	"Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II." Meka H., Werner F., Cordell S.C., Onesti S., Brick P. Nucleic Acids Res. 33:6435-6444(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF THE POL II RPB4-RPB7 SUBCOMPLEX.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U89387 Genomic DNA. Translation: AAC52056.1.
U85510 mRNA. Translation: AAC80226.1.
BC017205 mRNA. Translation: AAH17205.1.
BC093795 mRNA. Translation: AAH93795.1.
BC093797 mRNA. Translation: AAH93797.1.

IPI

IPI00007283.

RefSeq

NP_004796.1. NM_004805.3.

UniGene

Hs.715348.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2C35	X-ray	2.70	A/C/E/G	1-142	[»]

ProteinModelPortal

O15514.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-32912N.

IntAct

O15514. 8 interactions.

STRING

9606.ENSP00000272645.

PTM databases

PhosphoSite

O15514.

Proteomic databases

PaxDb

O15514.

PeptideAtlas

O15514.

PRIDE

O15514.

Protocols and materials databases

DNASU

5433.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000272645; ENSP00000272645; ENSG00000144231.

GeneID

5433.

KEGG

hsa:5433.

UCSC

uc002tpj.3. human.

Organism-specific databases

CTD

5433.

GeneCards

GC02M128620.

HGNC

HGNC:9191. POLR2D.

HPA

HPA046092.

MIM

606017. gene.

neXtProt

NX_O15514.

PharmGKB

PA33511.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5250.

HOGENOM

HOG000195281.

HOVERGEN

HBG002800.

InParanoid

O15514.

K03012.

OMA

SQLVFPK.

OrthoDB

EOG444KMN.

PhylomeDB

O15514.

Enzyme and pathway databases

Reactome

REACT_116125. Disease.
REACT_1675. mRNA Processing.
REACT_1788. Transcription.
REACT_1892. Elongation arrest and recovery.
REACT_216. DNA Repair.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

O15514.

Bgee

O15514.

CleanEx

HS_POLR2D.

Genevestigator

O15514.

GermOnline

ENSG00000144231. Homo sapiens.

Family and domain databases

InterPro

IPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]

Pfam

PF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]

SMART

SM00657. RPOL4c. 1 hit.
[Graphical view]

SUPFAM

SSF47819. HRDC_like. 1 hit.

ProtoNet

Search...

Other

ChiTaRS

POLR2D. human.

EvolutionaryTrace

O15514.

GenomeRNAi

5433.

NextBio

21021.

SOURCE

Search...

Entry information

Entry name

RPB4_HUMAN

Accession

Primary (citable) accession number: O15514
Secondary accession number(s): Q52LT4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	January 1, 1998
Last modified:	May 1, 2013
This is version 124 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

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

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents