DNA-directed RNA polymerase II subunit RPB4

NameDNA-directed RNA polymerase II subunit RPB4
Synonyms
  • DNA-directed RNA polymerase II subunit D
  • RNA polymerase II 16 kDa subunit
  • RNA polymerase II subunit B4
  • RPB16
Gene NamePOLR2D
OrganismHuman
Amino acid sequence
>lcl|BSEQ0012580|DNA-directed RNA polymerase II subunit RPB4
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY
Number of residues142
Molecular Weight16311.105
Theoretical pI4.46
GO Classification
Functions
  • DNA-directed RNA polymerase activity
  • nucleotide binding
  • translation initiation factor binding
Processes
  • mRNA splicing, via spliceosome
  • nucleotide-excision repair
  • piRNA metabolic process
  • transcription from RNA polymerase II promoter
  • positive regulation of translational initiation
  • positive regulation of viral transcription
  • gene expression
  • recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
  • transcription initiation from RNA polymerase II promoter
  • RNA splicing
  • transcription elongation from RNA polymerase II promoter
  • somatic stem cell population maintenance
  • transcription-coupled nucleotide-excision repair
  • viral process
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
  • 7-methylguanosine mRNA capping
  • gene silencing by RNA
  • DNA repair
  • mRNA export from nucleus in response to heat stress
Components
  • DNA-directed RNA polymerase II, core complex
  • nucleoplasm
  • cytoplasmic mRNA processing body
  • nucleus
General FunctionTranslation initiation factor binding
Specific FunctionDNA-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).
Pfam Domain Function
Transmembrane RegionsNot Available
GenBank Protein ID2253633
UniProtKB IDO15514
UniProtKB Entry NameRPB4_HUMAN
Cellular LocationNucleus
Gene sequence
>lcl|BSEQ0012581|DNA-directed RNA polymerase II subunit RPB4 (POLR2D)
ATGGCGGCGGGTGGCAGCGATCCGCGGGCTGGCGACGTAGAGGAGGACGCCTCACAGCTC
ATCTTTCCTAAAGAGTTTGAAACAGCTGAGACACTTCTAAATTCAGAAGTTCATATGCTT
CTGGAACATCGAAAGCAGCAGAATGAGAGTGCAGAGGACGAACAGGAGCTCTCAGAAGTC
TTCATGAAAACATTAAACTACACAGCCCGTTTCAGTCGTTTCAAAAACAGAGAGACCATT
GCCAGTGTTCGTAGCTTGCTACTCCAGAAAAAGCTTCATAAGTTTGAGTTGGCCTGTTTG
GCCAACCTTTGCCCAGAGACTGCTGAGGAGTCCAAGGCTCTAATCCCAAGCTTGGAGGGA
CGGTTTGAAGATGAGGAGCTGCAGCAGATTCTTGATGATATCCAGACAAAGCGCAGCTTT
CAGTATTAA
GenBank Gene IDU85510
GeneCard IDNot Available
GenAtlas IDNot Available
HGNC IDHGNC:9191
Chromosome Location2
Locus2q21
References
  1. Khazak V, Estojak J, Cho H, Majors J, Sonoda G, Testa JR, Golemis EA: Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II. Mol Cell Biol. 1998 Apr;18(4):1935-45. 9528765
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. 15489334
  3. Kershnar E, Wu SY, Chiang CM: 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. J Biol Chem. 1998 Dec 18;273(51):34444-53. 9852112
  4. Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Burckstummer T, Bennett KL, Superti-Furga G, Colinge J: Initial characterization of the human central proteome. BMC Syst Biol. 2011 Jan 26;5:17. doi: 10.1186/1752-0509-5-17. 21269460
  5. Meka H, Werner F, Cordell SC, Onesti S, Brick P: Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucleic Acids Res. 2005 Nov 10;33(19):6435-44. Print 2005. 16282592