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Protein

DNA-directed RNA polymerase I subunit RPA135

Gene

RPA135

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerases catalyze the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I (Pol I) which synthesizes ribosomal RNA precursors. Besides, RNA polymerase I has intrinsic RNA cleavage activity. RPA190 and RPA135 both contribute to the polymerase catalytic activity and together form the Pol I active center. In addition, subunit RPA12 contributes a catalytic zinc ribbon that is required for RNA cleavage by Pol I. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA190 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I 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.3 Publications

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1104 – 1131C4-typeAdd BLAST28

GO - Molecular functioni

  • DNA binding Source: InterPro
  • metal ion binding Source: UniProtKB-KW
  • ribonucleoside binding Source: InterPro
  • RNA polymerase I activity Source: UniProtKB

GO - Biological processi

  • ribosome biogenesis Source: UniProtKB-KW
  • transcription from RNA polymerase I promoter Source: UniProtKB
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, Transcription

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-34172-MONOMER.
ReactomeiR-SCE-73762. RNA Polymerase I Transcription Initiation.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase I subunit RPA135 (EC:2.7.7.6)
Alternative name(s):
DNA-directed RNA polymerase I 135 kDa polypeptide
Short name:
A135
DNA-directed RNA polymerase I polypeptide 2
Short name:
RNA polymerase I subunit 2
Gene namesi
Name:RPA135
Synonyms:RPA2, RRN2, SRP3
Ordered Locus Names:YPR010C
ORF Names:YP9531.03C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR010C.
SGDiS000006214. RPA135.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase I complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1104C → A: No effect; when associated with A-1107; A-1128 and A-1131. 1 Publication1
Mutagenesisi1107C → A: Lethal. Abolishes recruitment of RPA1 to Pol I. No effect; when associated with A-1104; A-1128 and A-1131. 1 Publication1
Mutagenesisi1127C → R: Responsible of suppression of RPA190-5 and RPA190-1 mutations. 1
Mutagenesisi1128C → A: No effect; when associated with A-1104; A-1107 and A-1131. 1 Publication1
Mutagenesisi1131C → A: No effect; when associated with A-1104; A-1107 and A-1128. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000480802 – 1203DNA-directed RNA polymerase I subunit RPA135Add BLAST1202

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei81PhosphoserineCombined sources1
Modified residuei1156PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP22138.
PRIDEiP22138.

PTM databases

iPTMnetiP22138.

Interactioni

Subunit structurei

Component of the RNA polymerase I (Pol I) complex consisting of 14 subunits: RPA135, RPA190, RPC40, RPA14, RPB5, RPO26, RPA43, RPB8, RPA12, RPB10, RPC19, RPC10, RPA49 and RPA34. The complex is composed of a horseshoe-shaped core containing ten subunits (RPA135, RPA190, RPB5, RPO26, RPB8, RPB10, RPC10, RPA12, RPC19 and RPC40) where RPA135 and RPA190 form the DNA-binding cleft. Outside of the core, RPA14 and RPA43 form the stalk that mediates interactions with transcription initiation factors and newly synthesized RNA.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RPA190P109644EBI-15736,EBI-15730

Protein-protein interaction databases

BioGridi36188. 141 interactors.
DIPiDIP-135N.
IntActiP22138. 51 interactors.
MINTiMINT-423299.

Structurei

Secondary structure

11203
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi18 – 26Combined sources9
Beta strandi30 – 32Combined sources3
Helixi36 – 50Combined sources15
Turni51 – 53Combined sources3
Helixi56 – 58Combined sources3
Helixi60 – 68Combined sources9
Beta strandi71 – 74Combined sources4
Helixi86 – 89Combined sources4
Beta strandi94 – 104Combined sources11
Beta strandi108 – 111Combined sources4
Beta strandi117 – 120Combined sources4
Helixi123 – 129Combined sources7
Beta strandi134 – 145Combined sources12
Turni146 – 149Combined sources4
Beta strandi150 – 162Combined sources13
Turni171 – 174Combined sources4
Helixi177 – 182Combined sources6
Beta strandi194 – 196Combined sources3
Beta strandi199 – 203Combined sources5
Beta strandi205 – 209Combined sources5
Beta strandi214 – 218Combined sources5
Helixi220 – 225Combined sources6
Beta strandi229 – 239Combined sources11
Beta strandi245 – 253Combined sources9
Beta strandi258 – 264Combined sources7
Beta strandi267 – 272Combined sources6
Helixi273 – 280Combined sources8
Helixi285 – 293Combined sources9
Helixi300 – 313Combined sources14
Turni314 – 316Combined sources3
Helixi323 – 334Combined sources12
Turni335 – 339Combined sources5
Beta strandi342 – 344Combined sources3
Helixi346 – 357Combined sources12
Helixi360 – 362Combined sources3
Helixi367 – 385Combined sources19
Beta strandi387 – 389Combined sources3
Helixi397 – 399Combined sources3
Beta strandi400 – 403Combined sources4
Helixi405 – 434Combined sources30
Helixi443 – 451Combined sources9
Helixi457 – 467Combined sources11
Beta strandi485 – 487Combined sources3
Helixi493 – 499Combined sources7
Beta strandi502 – 504Combined sources3
Helixi507 – 510Combined sources4
Turni516 – 518Combined sources3
Helixi522 – 524Combined sources3
Turni525 – 527Combined sources3
Turni537 – 541Combined sources5
Beta strandi542 – 545Combined sources4
Turni558 – 560Combined sources3
Helixi561 – 567Combined sources7
Helixi573 – 575Combined sources3
Beta strandi583 – 588Combined sources6
Beta strandi591 – 596Combined sources6
Helixi598 – 614Combined sources17
Beta strandi618 – 620Combined sources3
Beta strandi625 – 629Combined sources5
Beta strandi633 – 636Combined sources4
Beta strandi639 – 643Combined sources5
Beta strandi649 – 655Combined sources7
Turni656 – 659Combined sources4
Beta strandi660 – 664Combined sources5
Helixi666 – 669Combined sources4
Beta strandi674 – 677Combined sources4
Helixi678 – 680Combined sources3
Turni683 – 685Combined sources3
Beta strandi687 – 689Combined sources3
Helixi693 – 696Combined sources4
Helixi699 – 703Combined sources5
Helixi707 – 709Combined sources3
Helixi712 – 722Combined sources11
Helixi733 – 735Combined sources3
Beta strandi739 – 745Combined sources7
Beta strandi751 – 753Combined sources3
Helixi755 – 759Combined sources5
Helixi762 – 764Combined sources3
Beta strandi769 – 777Combined sources9
Beta strandi779 – 781Combined sources3
Beta strandi786 – 790Combined sources5
Helixi791 – 795Combined sources5
Turni796 – 799Combined sources4
Beta strandi801 – 810Combined sources10
Beta strandi813 – 815Combined sources3
Beta strandi823 – 826Combined sources4
Helixi835 – 838Combined sources4
Beta strandi844 – 846Combined sources3
Beta strandi857 – 863Combined sources7
Turni864 – 867Combined sources4
Beta strandi868 – 873Combined sources6
Beta strandi880 – 888Combined sources9
Beta strandi892 – 894Combined sources3
Beta strandi900 – 909Combined sources10
Beta strandi916 – 919Combined sources4
Beta strandi924 – 931Combined sources8
Turni933 – 935Combined sources3
Beta strandi938 – 942Combined sources5
Beta strandi946 – 949Combined sources4
Helixi951 – 953Combined sources3
Turni955 – 957Combined sources3
Helixi960 – 975Combined sources16
Beta strandi988 – 990Combined sources3
Helixi992 – 1003Combined sources12
Beta strandi1009 – 1011Combined sources3
Turni1016 – 1018Combined sources3
Beta strandi1026 – 1036Combined sources11
Helixi1040 – 1043Combined sources4
Beta strandi1045 – 1049Combined sources5
Turni1054 – 1056Combined sources3
Helixi1063 – 1065Combined sources3
Beta strandi1069 – 1071Combined sources3
Helixi1073 – 1082Combined sources10
Helixi1085 – 1092Combined sources8
Turni1093 – 1097Combined sources5
Beta strandi1098 – 1104Combined sources7
Turni1105 – 1107Combined sources3
Beta strandi1110 – 1115Combined sources6
Beta strandi1120 – 1122Combined sources3
Beta strandi1126 – 1131Combined sources6
Helixi1135 – 1139Combined sources5
Helixi1155 – 1157Combined sources3
Beta strandi1158 – 1160Combined sources3
Beta strandi1166 – 1168Combined sources3
Beta strandi1173 – 1179Combined sources7
Helixi1180 – 1191Combined sources12
Beta strandi1194 – 1201Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80B/Q1-1203[»]
4C3HX-ray3.27B1-1203[»]
4C3IX-ray3.0B1-1203[»]
4C3JX-ray3.35B1-1203[»]
4YM7X-ray5.50AB/BB/CB/DB/EB/FB1-1203[»]
5G5Lelectron microscopy4.80B1-1203[»]
ProteinModelPortaliP22138.
SMRiP22138.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1104 – 1131C4-typeAdd BLAST28

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00760000119399.
HOGENOMiHOG000222963.
InParanoidiP22138.
KOiK03002.
OMAiHTVRYDA.
OrthoDBiEOG092C06IY.

Family and domain databases

CDDicd00653. RNA_pol_B_RPB2. 1 hit.
Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
IPR009674. Rpa2_dom_4.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 2 hits.
PfamiPF06883. RNA_pol_Rpa2_4. 1 hit.
PF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P22138-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN
60 70 80 90 100
ALTEGPDGGL LNLGVKDIGE KVIFDGKPLN SEDEISNSGY LGNKLSVSVE
110 120 130 140 150
QVSIAKPMSN DGVSSAVERK VYPSESRQRL TSYRGKLLLK LKWSVNNGEE
160 170 180 190 200
NLFEVRDCGG LPVMLQSNRC HLNKMSPYEL VQHKEESDEI GGYFIVNGIE
210 220 230 240 250
KLIRMLIVQR RNHPMAIIRP SFANRGASYS HYGIQIRSVR PDQTSQTNVL
260 270 280 290 300
HYLNDGQVTF RFSWRKNEYL VPVVMILKAL CHTSDREIFD GIIGNDVKDS
310 320 330 340 350
FLTDRLELLL RGFKKRYPHL QNRTQVLQYL GDKFRVVFQA SPDQSDLEVG
360 370 380 390 400
QEVLDRIVLV HLGKDGSQDK FRMLLFMIRK LYSLVAGECS PDNPDATQHQ
410 420 430 440 450
EVLLGGFLYG MILKEKIDEY LQNIIAQVRM DINRGMAINF KDKRYMSRVL
460 470 480 490 500
MRVNENIGSK MQYFLSTGNL VSQSGLDLQQ VSGYTVVAEK INFYRFISHF
510 520 530 540 550
RMVHRGSFFA QLKTTTVRKL LPESWGFLCP VHTPDGSPCG LLNHFAHKCR
560 570 580 590 600
ISTQQSDVSR IPSILYSLGV APASHTFAAG PSLCCVQIDG KIIGWVSHEQ
610 620 630 640 650
GKIIADTLRY WKVEGKTPGL PIDLEIGYVP PSTRGQYPGL YLFGGHSRML
660 670 680 690 700
RPVRYLPLDK EDIVGPFEQV YMNIAVTPQE IQNNVHTHVE FTPTNILSIL
710 720 730 740 750
ANLTPFSDFN QSPRNMYQCQ MGKQTMGTPG VALCHRSDNK LYRLQTGQTP
760 770 780 790 800
IVKANLYDDY GMDNFPNGFN AVVAVISYTG YDMDDAMIIN KSADERGFGY
810 820 830 840 850
GTMYKTEKVD LALNRNRGDP ITQHFGFGND EWPKEWLEKL DEDGLPYIGT
860 870 880 890 900
YVEEGDPICA YFDDTLNKTK IKTYHSSEPA YIEEVNLIGD ESNKFQELQT
910 920 930 940 950
VSIKYRIRRT PQIGDKFSSR HGQKGVCSRK WPTIDMPFSE TGIQPDIIIN
960 970 980 990 1000
PHAFPSRMTI GMFVESLAGK AGALHGIAQD STPWIFNEDD TPADYFGEQL
1010 1020 1030 1040 1050
AKAGYNYHGN EPMYSGATGE ELRADIYVGV VYYQRLRHMV NDKFQVRSTG
1060 1070 1080 1090 1100
PVNSLTMQPV KGRKRHGGIR VGEMERDALI GHGTSFLLQD RLLNSSDYTQ
1110 1120 1130 1140 1150
ASVCRECGSI LTTQQSVPRI GSISTVCCRR CSMRFEDAKK LLTKSEDGEK
1160 1170 1180 1190 1200
IFIDDSQIWE DGQGNKFVGG NETTTVAIPF VLKYLDSELS AMGIRLRYNV

EPK
Length:1,203
Mass (Da):135,742
Last modified:August 1, 1991 - v1
Checksum:i72FA95B66F98C5F8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31900 Genomic DNA. Translation: AAA97589.1.
M62804 Genomic DNA. Translation: AAA34993.1.
Z49919 Genomic DNA. Translation: CAA90154.1.
Z71255 Genomic DNA. Translation: CAA95050.1.
BK006949 Genomic DNA. Translation: DAA11437.1.
PIRiA39607.
RefSeqiNP_015335.1. NM_001184107.1.

Genome annotation databases

EnsemblFungiiYPR010C; YPR010C; YPR010C.
GeneIDi856119.
KEGGisce:YPR010C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31900 Genomic DNA. Translation: AAA97589.1.
M62804 Genomic DNA. Translation: AAA34993.1.
Z49919 Genomic DNA. Translation: CAA90154.1.
Z71255 Genomic DNA. Translation: CAA95050.1.
BK006949 Genomic DNA. Translation: DAA11437.1.
PIRiA39607.
RefSeqiNP_015335.1. NM_001184107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80B/Q1-1203[»]
4C3HX-ray3.27B1-1203[»]
4C3IX-ray3.0B1-1203[»]
4C3JX-ray3.35B1-1203[»]
4YM7X-ray5.50AB/BB/CB/DB/EB/FB1-1203[»]
5G5Lelectron microscopy4.80B1-1203[»]
ProteinModelPortaliP22138.
SMRiP22138.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36188. 141 interactors.
DIPiDIP-135N.
IntActiP22138. 51 interactors.
MINTiMINT-423299.

PTM databases

iPTMnetiP22138.

Proteomic databases

MaxQBiP22138.
PRIDEiP22138.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR010C; YPR010C; YPR010C.
GeneIDi856119.
KEGGisce:YPR010C.

Organism-specific databases

EuPathDBiFungiDB:YPR010C.
SGDiS000006214. RPA135.

Phylogenomic databases

GeneTreeiENSGT00760000119399.
HOGENOMiHOG000222963.
InParanoidiP22138.
KOiK03002.
OMAiHTVRYDA.
OrthoDBiEOG092C06IY.

Enzyme and pathway databases

BioCyciYEAST:G3O-34172-MONOMER.
ReactomeiR-SCE-73762. RNA Polymerase I Transcription Initiation.

Miscellaneous databases

PROiP22138.

Family and domain databases

CDDicd00653. RNA_pol_B_RPB2. 1 hit.
Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
IPR009674. Rpa2_dom_4.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 2 hits.
PfamiPF06883. RNA_pol_Rpa2_4. 1 hit.
PF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPA2_YEAST
AccessioniPrimary (citable) accession number: P22138
Secondary accession number(s): D6W421
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: November 2, 2016
This is version 157 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Three distinct zinc-containing RNA polymerases are found in eukaryotic nuclei: polymerase I for the ribosomal RNA precursor, polymerase II for the mRNA precursor, and polymerase III for 5S and tRNA genes.
Present with 14100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

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.