DNA-directed RNA polymerase II subunit RPB4

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Reviewed, UniProtKB/Swiss-Prot O15514 (RPB4_HUMAN)

Last modified December 15, 2009. Version 93. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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
    DNA-directed RNA polymerase II 16 kDa polypeptide

Gene names

Name:

POLR2D

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

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

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Protein attributes

Sequence length	142 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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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.
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.
Subcellular location	Nucleus Ref.3.
Sequence similarities	Belongs to the eukaryotic RPB4 RNA polymerase subunit family.

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Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
PTM	Acetylation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA elongation from RNA polymerase II promoter Inferred from Experiment. Source: Reactome nuclear mRNA splicing, via spliceosome Inferred from Experiment. Source: Reactome transcription initiation from RNA polymerase II promoter Inferred from Experiment. Source: Reactome
Cellular component	DNA-directed RNA polymerase II, core complex Ref.1 Ref.3 Inferred from direct assay. Source: UniProtKB
Molecular function	DNA-directed RNA polymerase activity Ref.1 Inferred from mutant phenotype. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed

Chain

2 – 142

141

DNA-directed RNA polymerase II subunit RPB4

PRO_0000073981

Amino acid modifications

Modified residue

N-acetylalanine

Secondary structure

142

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

O15514-1 [UniParc].

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

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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: 9528765] [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: 15489334] [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: 9852112] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II CORE-COMPLEX, SUBCELLULAR LOCATION.
[4]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY.
[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: 16282592] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF THE POL II RPB4-RPB7 SUBCOMPLEX.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

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.

UniGene

Hs.554831

3D structure databases

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

ModBase

Search...

Protein-protein interaction databases

IntAct

O15514. 7 interactions.

STRING

O15514.

PTM databases

PhosphoSite

O15514.

Proteomic databases

PeptideAtlas

O15514.

PRIDE

O15514.

Genome annotation databases

Ensembl

ENST00000272645; ENSP00000272645; ENSG00000144231; Homo sapiens. [Genome view]

GeneID

5433.

KEGG

hsa:5433.

UCSC

uc002tpj.1. human.

Organism-specific databases

CTD

5433.

GeneCards

GC02M128320.

H-InvDB

HIX0021308.

HGNC

HGNC:9191. POLR2D.

MIM

606017. gene.

PharmGKB

PA33511.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

HBG592325.

HOVERGEN

O15514.

InParanoid

O15514.

OMA

CLMNCEV.

OrthoDB

EOG95HVHX.

Enzyme and pathway databases

Reactome

REACT_12472. Regulatory RNA pathways.
REACT_125. Processing of Capped Intron-Containing Pre-mRNA.
REACT_1675. mRNA Processing.
REACT_1788. Transcription.
REACT_1892. Elongation arrest and recovery.
REACT_216. DNA Repair.
REACT_6143. Pausing and recovery of Tat-mediated HIV-1 elongation.
REACT_6167. Influenza Infection.
REACT_6185. HIV Infection.
REACT_6244. Pausing and recovery of HIV-1 elongation.
REACT_6259. HIV-1 elongation arrest and recovery.
REACT_6344. Tat-mediated HIV-1 elongation arrest and recovery.
REACT_71. Gene Expression.
REACT_769. Pausing and recovery of elongation.

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]

ProtoNet

Search...

Other Resources

NextBio

21021.

SOURCE

Search...

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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:	December 15, 2009
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.

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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