P34087 (RPB7_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB7
Short name=RNA polymerase II subunit B7

Alternative name(s):
B16

Gene names

Name:	RPB7
Ordered Locus Names:	YDR404C
ORF Names:	D9509.22

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	171 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. RPB7 is part of a subcomplex with RPB4 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. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II. Ref.5 Ref.6 Ref.10
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. The RPB4-RPB7 subcomplex probably associates with TFG1. Interacts with NRD1 and PAT1. Ref.8 Ref.9 Ref.10
Subcellular location	Nucleus. Cytoplasm. Cytoplasm › P-body. Note: Seems to shuttle between nucleus and cytoplasm in a complex with RPB4. Ref.7 Ref.10
Miscellaneous	Present with 6420 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the eukaryotic RPB7/RPC8 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	Cytoplasm DNA-directed RNA polymerase Nucleus
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	nuclear-transcribed mRNA catabolic process, exonucleolytic Inferred from genetic interaction Ref.10. Source: SGD positive regulation of nuclear-transcribed mRNA poly(A) tail shortening Inferred from mutant phenotype Ref.10. Source: SGD positive regulation of translational initiation Inferred from mutant phenotype PubMed 21074047. Source: SGD transcription initiation from RNA polymerase II promoter Inferred from direct assay Ref.5. Source: SGD
Cellular_component	DNA-directed RNA polymerase II, core complex Inferred from direct assay PubMed 1331084PubMed 2183013PubMed 2186966. Source: SGD cytoplasmic mRNA processing body Inferred from direct assay Ref.10. Source: SGD
Molecular_function	DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW single-stranded DNA binding Inferred from direct assay Ref.5. Source: SGD single-stranded RNA binding Inferred from direct assay Ref.5. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RPB4	P20433	4	EBI-15790,EBI-15777

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 171

171

DNA-directed RNA polymerase II subunit RPB7

PRO_0000073993

Experimental info

Mutagenesis

108 – 113

6

Missing: Lowers nucleic-acid binding of RPB4-RPB7 by 10-fold; no effect on association with Pol II core complex; abolishes transcriptional activity of Pol II. Ref.5

Mutagenesis

151 – 158

8

Missing: No effect on nucleic-acid binding of RPB4-RPB7 and on association with Pol II core complex; abolishes transcriptional activity of Pol II. Ref.5

Secondary structure

1

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171

Helix Strand Turn

Details...

Beta strand

2 – 10

9

Helix

15 – 17

3

Beta strand

19 – 21

3

Helix

22 – 34

13

Beta strand

37 – 39

3

Turn

40 – 42

3

Beta strand

43 – 48

6

Helix

51 – 53

3

Beta strand

59 – 61

3

Beta strand

63 – 65

3

Beta strand

71 – 79

9

Beta strand

86 – 95

10

Beta strand

98 – 103

6

Beta strand

106 – 111

6

Helix

112 – 114

3

Beta strand

117 – 122

6

Beta strand

124 – 127

4

Beta strand

129 – 131

3

Beta strand

136 – 138

3

Beta strand

142 – 153

12

Beta strand

156 – 162

7

Beta strand

165 – 167

3

Sequences

	Sequence		Length	Mass (Da)
	P34087 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: 44C85603A93CDE67	FASTA	171	19,058
	10 20 30 40 50 60 MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR 70 80 90 100 110 120 ILPTDGSAEF NVKYRAVVFK PFKGEVVDGT VVSCSQHGFE VQVGPMKVFV TKHLMPQDLT 130 140 150 160 170 FNAGSNPPSY QSSEDVITIK SRIRVKIEGC ISQVSSIHAI GSIKEDYLGA I

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"RPB7, one of two dissociable subunits of yeast RNA polymerase II, is essential for cell viability." McKune K., Richards K.L., Edwards A.M., Young R.A., Woychik N.A. Yeast 9:295-299(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]	"Dissociable Rpb4-Rpb7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation." Orlicky S.M., Tran P.T., Sayre M.H., Edwards A.M. J. Biol. Chem. 276:10097-10102(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RPB4-RPB7 COMPLEX, RNA-BINDING, MUTAGENESIS OF 108-VAL--HIS-113 AND 151-ILE--HIS-158.
[6]	"Structure and mechanism of RNA polymerase II CTD phosphatases." Kamenski T., Heilmeier S., Meinhart A., Cramer P. Mol. Cell 15:399-407(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RPB4-RPB7 COMPLEX.
[7]	"Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways." Selitrennik M., Duek L., Lotan R., Choder M. Eukaryot. Cell 5:2092-2103(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts." Mitsuzawa H., Kanda E., Ishihama A. Nucleic Acids Res. 31:4696-4701(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NRD1.
[9]	"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex." Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J. Mol. Cell 12:1003-1013(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX, INTERACTION WITH TFG1.
[10]	"The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms." Lotan R., Goler-Baron V., Duek L., Haimovich G., Choder M. J. Cell Biol. 178:1133-1143(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PAT1.
[11]	"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage." Kettenberger H., Armache K.J., Cramer P. Cell 114:347-357(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
[12]	"Architecture of initiation-competent 12-subunit RNA polymerase II." Armache K.J., Kettenberger H., Cramer P. Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
[13]	"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS." Kettenberger H., Armache K.J., Cramer P. Mol. Cell 16:955-965(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II COMPLEX.
[14]	"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7." Armache K.J., Mitterweger S., Meinhart A., Cramer P. J. Biol. Chem. 280:7131-7134(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
[15]	"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs." Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P. Nat. Struct. Mol. Biol. 13:44-48(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
[16]	"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model." Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J. Structure 14:973-982(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

S59775 Genomic DNA. Translation: AAC60558.1.
U32274 Genomic DNA. Translation: AAB64844.1.
BK006938 Genomic DNA. Translation: DAA12246.1.

PIR

S30140.

RefSeq

NP_010692.3. NM_001180712.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NT9	X-ray	4.20	G	1-171	[»]
1PQV	X-ray	3.80	G	1-171	[»]
1WCM	X-ray	3.80	G	1-171	[»]
1Y14	X-ray	2.30	B/D	1-171	[»]
1Y1V	X-ray	3.80	G	1-171	[»]
1Y1W	X-ray	4.00	G	1-171	[»]
1Y1Y	X-ray	4.00	G	1-171	[»]
1Y77	X-ray	4.50	G	1-171	[»]
2B63	X-ray	3.80	G	1-171	[»]
2B8K	X-ray	4.15	G	1-171	[»]
2JA5	X-ray	3.80	G	1-171	[»]
2JA6	X-ray	4.00	G	1-171	[»]
2JA7	X-ray	3.80	G/S	1-171	[»]
2JA8	X-ray	3.80	G	1-171	[»]
2R7Z	X-ray	3.80	G	1-171	[»]
2R92	X-ray	3.80	G	1-171	[»]
2R93	X-ray	4.00	G	1-171	[»]
2VUM	X-ray	3.40	G	1-171	[»]
3FKI	X-ray	3.88	G	1-171	[»]
3H3V	X-ray	4.00	H	1-171	[»]
3HOU	X-ray	3.20	G/S	1-171	[»]
3HOV	X-ray	3.50	G	1-171	[»]
3HOW	X-ray	3.60	G	1-171	[»]
3HOX	X-ray	3.65	G	1-171	[»]
3HOY	X-ray	3.40	G	1-171	[»]
3HOZ	X-ray	3.65	G	1-171	[»]
3I4M	X-ray	3.70	G	1-171	[»]
3I4N	X-ray	3.90	G	1-171	[»]
3J1N	electron microscopy	16.00	G	1-171	[»]
3K1F	X-ray	4.30	G	1-171	[»]
3PO2	X-ray	3.30	G	1-171	[»]
3PO3	X-ray	3.30	G	1-171	[»]
3QT1	X-ray	4.30	G	1-171	[»]
4A3B	X-ray	3.50	G	1-171	[»]
4A3C	X-ray	3.50	G	1-171	[»]
4A3D	X-ray	3.40	G	1-171	[»]
4A3E	X-ray	3.40	G	1-171	[»]
4A3F	X-ray	3.50	G	1-171	[»]
4A3G	X-ray	3.50	G	1-171	[»]
4A3I	X-ray	3.80	G	1-171	[»]
4A3J	X-ray	3.70	G	1-171	[»]
4A3K	X-ray	3.50	G	1-171	[»]
4A3L	X-ray	3.50	G	1-171	[»]
4A3M	X-ray	3.90	G	1-171	[»]
4A93	X-ray	3.40	G	1-171	[»]
4BBR	X-ray	3.40	G	1-171	[»]
4BBS	X-ray	3.60	G	1-171	[»]

ProteinModelPortal

P34087.

SMR

P34087. Positions 1-171.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-725N.

IntAct

P34087. 23 interactions.

MINT

MINT-539630.

STRING

4932.YDR404C.

Proteomic databases

PaxDb

P34087.

PeptideAtlas

P34087.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR404C; YDR404C; YDR404C.

GeneID

852013.

KEGG

sce:YDR404C.
sce:YDR408C.

Organism-specific databases

CYGD

YDR404c.

SGD

S000002812. RPB7.

Phylogenomic databases

eggNOG

COG1095.

GeneTree

ENSGT00390000008975.

HOGENOM

HOG000158201.

KO

K00601.
K03015.

OMA

HAIGSIK.

OrthoDB

EOG4JT3FQ.

Gene expression databases

Genevestigator

P34087.

GermOnline

YDR404C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.
3.30.1490.120. 1 hit.

InterPro

IPR012340. NA-bd_OB-fold.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR022967. RNA-binding_domain_S1.
IPR005576. RNA_pol_Rpb7_N.
[Graphical view]

Pfam

PF00575. S1. 1 hit.
PF03876. SHS2_Rpb7-N. 1 hit.
[Graphical view]

SMART

SM00316. S1. 1 hit.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.
SSF88798. RNA_pol_Rpb7_N. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P34087.

NextBio

970216.

Entry information

Entry name

RPB7_YEAST

Accession

Primary (citable) accession number: P34087
Secondary accession number(s): D6VT36

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	May 1, 2013
This is version 125 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program