RNA polymerase-2 selections

RNA polymerase-2

Function: - RNA polymerase 2 transcribes genes into mRNA at ~ 50 bases/sec - synthesis of mRNA, snRNAs U1-U5 & U7 - at the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of RNA polymerase 2 - a bridging helix emanates from POLR2A & crosses the cleft near the catalytic site & is thought to promote translocation of RNA polymerase 2 by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition - during transcription elongation, RNA polymerase 2 moves on the template as the transcript elongates - elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of POLR2A which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination & mRNA processing - binding of ribonucleoside triphosphate to the RNA polymerase 2 transcribing complex probably involves a two- step mechanism - initial binding seems to occur at the entry (E) site & involves a Mg⁺² temporarily coordinated by 3 conserved Asp of the two largest RNA polymerase 2 subunits (POLR2A & POLR2B) - the ribonucleoside triphosphate is transferred by a rotation to the nucelotide addition (A) site for pairing with the template DNA - the catalytic A site involves 3 conserved Asp of POLR2A permanently coordinating a 2nd Mg⁺² - RNA polymerase 2 interacts with accessory proteins that modulate transcription including: a) elongation factor ELL2 b) transcription elongation factors necessary for efficient RNA polymerase 2 transcription elongation past template- encoded arresting sites - holoenzyme contains RNA polymerase 2 elongator complex Structure: - 12 subunits - yeast RNA polymerase 2 complex consists of 12 subunits all of which have been cloned - in mammalian systems many subunit genes have not yet been cloned - 2 largest subunits comprise at least part of the catalytic site, but the functions of other subunits are not yet clear - consist of core element with a central large cleft, a clamp element that moves to open & close the cleft & jaws that are thought to grab the incoming DNA template - the RNA polymerase 2 core element consists of POLR2A & POLR2B (2 largest subunits)

Interactions

molecular events

General

phosphoprotein regulatory molecule RNA polymerase

Properties

SUBUNITS: RNA polymerase-2 L' MOTIF: Zn finger C2H2-type SITE: 71-87 EFFECTOR-BOUND: Zn+2 MOTIF: Zn+2-binding site SITE: 71-71 Zn+2-binding site SITE: 74-74 Zn+2-binding site SITE: 81-81 Zn+2-binding site SITE: 84-84 Zn+2-binding site SITE: 111-111 Zn+2-binding site SITE: 114-114 Tyr phosphorylation site {Y145} Zn+2-binding site SITE: 154-154 Zn+2-binding site SITE: 184-184 Mg+2-binding site SITE: 495-495 Mg+2-binding site SITE: 497-497 Mg+2-binding site SITE: 499-499 Bridging helix {833-845} repeat {1593-1960} MOTIF: consensus repeat {1593-1960} SEQUENCE-IS: Y-[ST]-P-[STQ]-[ST]-P-[SRTEVKGN] Ser phosphorylation site {S1878} Tyr phosphorylation site {Y1923} Ser phosphorylation site {S1927} Thr phosphorylation site {T1933} Ser phosphorylation site {S1934} RNA polymerase-2 L MOTIF: Mg+2-binding site SITE: 792-792 Zn finger C4-type SITE: 1119-1140 EFFECTOR-BOUND: Zn+2 MOTIF: Zn+2-binding site SITE: 1119-1119 Zn+2-binding site SITE: 1122-1122 Zn+2-binding site SITE: 1137-1137 Zn+2-binding site SITE: 1140-1140 RNA polymerase-2 p33 MOTIF: cysteine-rich region {88-97} RNA polymerases 1, 2, & 3 subunit RPABC1 RNA polymerase-2 p19 RNA polymerase-2 p16 RNA polymerase 2 subunit RPB9 MOTIF: Zn finger C4-type SITE: 17-42 EFFECTOR-BOUND: Zn+2 MOTIF: Zn+2-binding site SITE: 17-17 Zn+2-binding site SITE: 20-20 Zn+2-binding site SITE: 39-39 Zn+2-binding site SITE: 42-42 Ser phosphorylation site {S73} Zinc finger NAME: Zinc finger SITE: 82-124 EFFECTOR-BOUND: Zn+2 MOTIF: Zn+2-binding site SITE: 86-86 Zn+2-binding site SITE: 89-89 Zn+2-binding site SITE: 114-114 Zn+2-binding site SITE: 119-119 RNA polymerases 1, 2, & 3 subunit RPABC2 MOTIF: Ser phosphorylation site {S2} RNA polymerase-2 p13.3 DNA-directed RNA polymerases 1, 2, & 3 subunit RPABC5 MOTIF: Zn+2-binding site SITE: 7-7 Zn+2-binding site SITE: 10-10 Zn+2-binding site SITE: 44-44 Zn+2-binding site SITE: 45-45 RNA polymerase 1, 2, 3 17.1 kD subunit (RPABC3, RPB17, RPB8, hRPB8, POLR2H) RNA polymerase I, 2, 2 7.0 kD subunit MOTIF: Zn finger C4-type SITE: 19-39 EFFECTOR-BOUND: Zn+2 RNA polymerase 2-associated protein 1 COMPARTMENT: cell nucleus MOTIF: Ser phosphorylation site {S603} Thr phosphorylation site {T1116}

References

UI89295557
Buratowski S. The basics of basal transcription by RNA polymerase II. Cell. 1994 Apr 8;77(1):1-3. Review. PMID: 8156586

Component-of

Tat-SF complex

Components

DNA-directed RNA polymerases 1, 2, & 3 subunit RPABC5 (RNA polymerase 2 p7.6 kD subunit, RPB10, RPB7.6, RNA polymerase 2 subunit L, POLR2L, RPABC5) RNA polymerase 1, 2, 3 17.1 kD subunit (RPABC3, RPB17, RPB8, hRPB8, POLR2H) RNA polymerase 2 13.3 kD subunit; RPB11; RPB11a; RNA polymerase 2 subunit J (POLR2J, POLR2J1) RNA polymerase 2 140 kD subunit (RPB2, RNA polymerase 2 subunit B, RNA polymerase 2 subunit 2, POLR2B) RNA polymerase 2 33 kD subunit (RPB33, RPB31, RNA polymerase 2 subunit C, POLR2C) RNA polymerase 2 largest subunit; RPB1; RNA polymerase 2 subunit A; RNA polymerase 2 subunit B1 (POLR2A) RNA polymerase 2 p16 kD subunit (RPB4, RNA polymerase 2 subunit D, POLR2D) RNA polymerase 2 p19 kD subunit (RPB7, RNA polymerase 2 subunit G, POLR2G) RNA polymerase 2 subunit RPB9 (RNA polymerase II p14.5 kD subunit, RPB14.5, RNA polymerase 2 subunit I, POLR2I, RPB9) RNA polymerase 2-associated protein 1 (RPAP1, KIAA1403) RNA polymerase I, 2, 2 7.0 kD subunit RNA polymerase II elongation factor ELL3 (ELL3) RNA polymerase II subunit A C-terminal domain phosphatase; TFIIF-associating CTD phosphatase (CTDP1, FCP1) RNA polymerases 1, 2, & 3 subunit RPABC1 (RNA polymerases 1, 2, & 3 subunit ABC1, RNA polymerase 2 23 kD subunit, RNA polymerase 2 subunit E, RNA polymerase 2 subunit 5, POLR2E, RPABC1, RPB25, RBP5, XAP4) RNA polymerases 1, 2, & 3 subunit RPABC2 (RPB6, RNA polymerase 2 subunit F, POLR2F, POLRF, ABC2, RPABC14.4, RPB14.4, RPC15) TBP-associated factor 2N; RNA-binding protein 56; RBP56; TAF15 RNA polymerase 2; TATA box-binding protein-associated factor 68-kd (TAF2N)

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