3H3V

Yeast RNAP II containing poly(A)-signal sequence in the active site

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001055	molecular_function	RNA polymerase II activity
B	0001172	biological_process	RNA-templated transcription
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0003968	molecular_function	RNA-dependent RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005665	cellular_component	RNA polymerase II, core complex
B	0005739	cellular_component	mitochondrion
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0010494	cellular_component	cytoplasmic stress granule
B	0016779	molecular_function	nucleotidyltransferase activity
B	0019985	biological_process	translesion synthesis
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001055	molecular_function	RNA polymerase II activity
C	0001172	biological_process	RNA-templated transcription
C	0003677	molecular_function	DNA binding
C	0003729	molecular_function	mRNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0003968	molecular_function	RNA-dependent RNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005665	cellular_component	RNA polymerase II, core complex
C	0005739	cellular_component	mitochondrion
C	0006351	biological_process	DNA-templated transcription
C	0006366	biological_process	transcription by RNA polymerase II
C	0006367	biological_process	transcription initiation at RNA polymerase II promoter
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0008270	molecular_function	zinc ion binding
C	0010494	cellular_component	cytoplasmic stress granule
C	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
C	0046872	molecular_function	metal ion binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0001055	molecular_function	RNA polymerase II activity
D	0001172	biological_process	RNA-templated transcription
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
D	0003968	molecular_function	RNA-dependent RNA polymerase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005665	cellular_component	RNA polymerase II, core complex
D	0006351	biological_process	DNA-templated transcription
D	0006366	biological_process	transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0006368	biological_process	transcription elongation by RNA polymerase II
D	0006369	biological_process	termination of RNA polymerase II transcription
D	0008270	molecular_function	zinc ion binding
D	0046872	molecular_function	metal ion binding
D	0046983	molecular_function	protein dimerization activity
D	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
E	0000166	molecular_function	nucleotide binding
E	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0000932	cellular_component	P-body
E	0001172	biological_process	RNA-templated transcription
E	0003697	molecular_function	single-stranded DNA binding
E	0003727	molecular_function	single-stranded RNA binding
E	0003968	molecular_function	RNA-dependent RNA polymerase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005665	cellular_component	RNA polymerase II, core complex
E	0005737	cellular_component	cytoplasm
E	0006352	biological_process	DNA-templated transcription initiation
E	0006366	biological_process	transcription by RNA polymerase II
E	0006367	biological_process	transcription initiation at RNA polymerase II promoter
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0006397	biological_process	mRNA processing
E	0030880	cellular_component	RNA polymerase complex
E	0031369	molecular_function	translation initiation factor binding
E	0044237	biological_process	cellular metabolic process
E	0045948	biological_process	positive regulation of translational initiation
E	1990328	cellular_component	RPB4-RPB7 complex
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001054	molecular_function	RNA polymerase I activity
F	0001055	molecular_function	RNA polymerase II activity
F	0001056	molecular_function	RNA polymerase III activity
F	0001172	biological_process	RNA-templated transcription
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
F	0003968	molecular_function	RNA-dependent RNA polymerase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005736	cellular_component	RNA polymerase I complex
F	0006351	biological_process	DNA-templated transcription
F	0006360	biological_process	transcription by RNA polymerase I
F	0006361	biological_process	transcription initiation at RNA polymerase I promoter
F	0006362	biological_process	transcription elongation by RNA polymerase I
F	0006363	biological_process	termination of RNA polymerase I transcription
F	0006366	biological_process	transcription by RNA polymerase II
F	0006367	biological_process	transcription initiation at RNA polymerase II promoter
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006383	biological_process	transcription by RNA polymerase III
F	0006384	biological_process	transcription initiation at RNA polymerase III promoter
F	0006386	biological_process	termination of RNA polymerase III transcription
F	0042254	biological_process	ribosome biogenesis
F	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
F	0042797	biological_process	tRNA transcription by RNA polymerase III
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0001054	molecular_function	RNA polymerase I activity
G	0001055	molecular_function	RNA polymerase II activity
G	0001056	molecular_function	RNA polymerase III activity
G	0001172	biological_process	RNA-templated transcription
G	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
G	0003968	molecular_function	RNA-dependent RNA polymerase activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005665	cellular_component	RNA polymerase II, core complex
G	0005666	cellular_component	RNA polymerase III complex
G	0005736	cellular_component	RNA polymerase I complex
G	0005737	cellular_component	cytoplasm
G	0006351	biological_process	DNA-templated transcription
G	0006360	biological_process	transcription by RNA polymerase I
G	0006361	biological_process	transcription initiation at RNA polymerase I promoter
G	0006362	biological_process	transcription elongation by RNA polymerase I
G	0006363	biological_process	termination of RNA polymerase I transcription
G	0006366	biological_process	transcription by RNA polymerase II
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0006383	biological_process	transcription by RNA polymerase III
G	0006384	biological_process	transcription initiation at RNA polymerase III promoter
G	0006386	biological_process	termination of RNA polymerase III transcription
G	0042254	biological_process	ribosome biogenesis
G	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
G	0042797	biological_process	tRNA transcription by RNA polymerase III
H	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0000932	cellular_component	P-body
H	0000956	biological_process	nuclear-transcribed mRNA catabolic process
H	0001172	biological_process	RNA-templated transcription
H	0003676	molecular_function	nucleic acid binding
H	0003697	molecular_function	single-stranded DNA binding
H	0003727	molecular_function	single-stranded RNA binding
H	0003968	molecular_function	RNA-dependent RNA polymerase activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005665	cellular_component	RNA polymerase II, core complex
H	0005737	cellular_component	cytoplasm
H	0006351	biological_process	DNA-templated transcription
H	0006352	biological_process	DNA-templated transcription initiation
H	0006366	biological_process	transcription by RNA polymerase II
H	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0006368	biological_process	transcription elongation by RNA polymerase II
H	0031369	molecular_function	translation initiation factor binding
H	0045948	biological_process	positive regulation of translational initiation
H	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
H	0060213	biological_process	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
H	1990328	cellular_component	RPB4-RPB7 complex
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001054	molecular_function	RNA polymerase I activity
I	0001055	molecular_function	RNA polymerase II activity
I	0001056	molecular_function	RNA polymerase III activity
I	0001172	biological_process	RNA-templated transcription
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0003968	molecular_function	RNA-dependent RNA polymerase activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005665	cellular_component	RNA polymerase II, core complex
I	0005666	cellular_component	RNA polymerase III complex
I	0005736	cellular_component	RNA polymerase I complex
I	0006351	biological_process	DNA-templated transcription
I	0006360	biological_process	transcription by RNA polymerase I
I	0006361	biological_process	transcription initiation at RNA polymerase I promoter
I	0006362	biological_process	transcription elongation by RNA polymerase I
I	0006363	biological_process	termination of RNA polymerase I transcription
I	0006366	biological_process	transcription by RNA polymerase II
I	0006367	biological_process	transcription initiation at RNA polymerase II promoter
I	0006368	biological_process	transcription elongation by RNA polymerase II
I	0006383	biological_process	transcription by RNA polymerase III
I	0006384	biological_process	transcription initiation at RNA polymerase III promoter
I	0006386	biological_process	termination of RNA polymerase III transcription
I	0042254	biological_process	ribosome biogenesis
I	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
I	0042797	biological_process	tRNA transcription by RNA polymerase III
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001172	biological_process	RNA-templated transcription
J	0001193	biological_process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
J	0003676	molecular_function	nucleic acid binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0003968	molecular_function	RNA-dependent RNA polymerase activity
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005730	cellular_component	nucleolus
J	0006281	biological_process	DNA repair
J	0006283	biological_process	transcription-coupled nucleotide-excision repair
J	0006351	biological_process	DNA-templated transcription
J	0006366	biological_process	transcription by RNA polymerase II
J	0006367	biological_process	transcription initiation at RNA polymerase II promoter
J	0006368	biological_process	transcription elongation by RNA polymerase II
J	0008270	molecular_function	zinc ion binding
J	0046872	molecular_function	metal ion binding
J	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0001054	molecular_function	RNA polymerase I activity
K	0001055	molecular_function	RNA polymerase II activity
K	0001056	molecular_function	RNA polymerase III activity
K	0001172	biological_process	RNA-templated transcription
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0003968	molecular_function	RNA-dependent RNA polymerase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005665	cellular_component	RNA polymerase II, core complex
K	0005666	cellular_component	RNA polymerase III complex
K	0005730	cellular_component	nucleolus
K	0005736	cellular_component	RNA polymerase I complex
K	0006351	biological_process	DNA-templated transcription
K	0006360	biological_process	transcription by RNA polymerase I
K	0006361	biological_process	transcription initiation at RNA polymerase I promoter
K	0006362	biological_process	transcription elongation by RNA polymerase I
K	0006363	biological_process	termination of RNA polymerase I transcription
K	0006366	biological_process	transcription by RNA polymerase II
K	0006367	biological_process	transcription initiation at RNA polymerase II promoter
K	0006368	biological_process	transcription elongation by RNA polymerase II
K	0006383	biological_process	transcription by RNA polymerase III
K	0006384	biological_process	transcription initiation at RNA polymerase III promoter
K	0006386	biological_process	termination of RNA polymerase III transcription
K	0008270	molecular_function	zinc ion binding
K	0042254	biological_process	ribosome biogenesis
K	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
K	0042797	biological_process	tRNA transcription by RNA polymerase III
K	0046872	molecular_function	metal ion binding
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001055	molecular_function	RNA polymerase II activity
L	0001172	biological_process	RNA-templated transcription
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
L	0003968	molecular_function	RNA-dependent RNA polymerase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005665	cellular_component	RNA polymerase II, core complex
L	0006351	biological_process	DNA-templated transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0006367	biological_process	transcription initiation at RNA polymerase II promoter
L	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006369	biological_process	termination of RNA polymerase II transcription
L	0046983	molecular_function	protein dimerization activity
M	0000428	cellular_component	DNA-directed RNA polymerase complex
M	0001054	molecular_function	RNA polymerase I activity
M	0001055	molecular_function	RNA polymerase II activity
M	0001056	molecular_function	RNA polymerase III activity
M	0001172	biological_process	RNA-templated transcription
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
M	0003968	molecular_function	RNA-dependent RNA polymerase activity
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005665	cellular_component	RNA polymerase II, core complex
M	0005666	cellular_component	RNA polymerase III complex
M	0005730	cellular_component	nucleolus
M	0005736	cellular_component	RNA polymerase I complex
M	0005737	cellular_component	cytoplasm
M	0005777	cellular_component	peroxisome
M	0006351	biological_process	DNA-templated transcription
M	0006360	biological_process	transcription by RNA polymerase I
M	0006361	biological_process	transcription initiation at RNA polymerase I promoter
M	0006362	biological_process	transcription elongation by RNA polymerase I
M	0006363	biological_process	termination of RNA polymerase I transcription
M	0006366	biological_process	transcription by RNA polymerase II
M	0006367	biological_process	transcription initiation at RNA polymerase II promoter
M	0006368	biological_process	transcription elongation by RNA polymerase II
M	0006383	biological_process	transcription by RNA polymerase III
M	0006384	biological_process	transcription initiation at RNA polymerase III promoter
M	0006386	biological_process	termination of RNA polymerase III transcription
M	0008270	molecular_function	zinc ion binding
M	0042254	biological_process	ribosome biogenesis
M	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
M	0042797	biological_process	tRNA transcription by RNA polymerase III
M	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 1734

Chain	Residue
B	CYS107
B	MET108
B	CYS110
B	CYS148
B	CYS167

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 1735

Chain	Residue
B	CYS67
B	CYS70
B	CYS77
B	HIS80

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 1225

Chain	Residue
C	CYS1163
C	CYS1166
C	CYS1182
C	CYS1185

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 319

Chain	Residue
D	CYS86
D	CYS88
D	CYS92
D	CYS95

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 123

Chain	Residue
J	CYS7
J	CYS10
J	CYS29
J	CYS32

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 124

Chain	Residue
J	CYS75
J	CYS78
J	CYS103
J	CYS106
J	HIS108

---

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 71

Chain	Residue
K	CYS7
K	CYS10
K	CYS45
K	CYS46

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN M 71

Chain	Residue
M	CYS31
M	CYS34
M	CYS48
M	CYS51

---

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG B 1736

Chain	Residue
B	ASP481
B	ASP483
B	ASP485
P	A10

---

Functional Information from PROSITE/UniProt

site_id	PS00115
Number of Residues	7
Details	RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA

Chain	Residue	Details
B	TYR1549-ALA1555
B	TYR1612-SER1618
B	TYR1619-SER1625
B	TYR1626-SER1632
B	TYR1633-SER1639
B	TYR1640-SER1646
B	TYR1647-SER1653
B	TYR1654-ALA1660
B	TYR1661-SER1667
B	TYR1668-SER1674
B	TYR1675-SER1681
B	TYR1556-SER1562
B	TYR1682-SER1688
B	TYR1689-ASN1695
B	TYR1696-SER1702
B	TYR1563-SER1569
B	TYR1570-SER1576
B	TYR1577-SER1583
B	TYR1584-SER1590
B	TYR1591-SER1597
B	TYR1598-SER1604
B	TYR1605-SER1611

---

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP

Chain	Residue	Details
D	ASN31-PRO71

---

site_id	PS00466
Number of Residues	36
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF

Chain	Residue	Details
J	CYS75-PHE110

---

site_id	PS01030
Number of Residues	27
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCRDCNNMLypredkennrllfeCrtC

Chain	Residue	Details
J	PHE6-CYS32

---

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE

Chain	Residue	Details
F	HIS147-GLU160

---

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ

Chain	Residue	Details
G	THR86-GLN100

---

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG

Chain	Residue	Details
K	ILE2-GLY11

---

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP

Chain	Residue	Details
L	PHE35-PRO66

---

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT

Chain	Residue	Details
C	GLY977-THR989

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	20
Details	ZN_FING: C4-type

Chain	Residue	Details
M	CYS31-CYS51
B	ASP483
B	ASP485
K	CYS10
K	CYS45
K	CYS46
B	CYS107
B	CYS110
B	CYS148
B	CYS167
B	ASP481

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING:

Chain	Residue	Details
M	CYS31
M	CYS34
M	CYS48
M	CYS51
C	CYS1185

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499

Chain	Residue	Details
J	CYS7
J	CYS10
J	CYS29
J	CYS32

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499

Chain	Residue	Details
J	CYS75
J	CYS78
J	CYS103
J	CYS106

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956

Chain	Residue	Details
J	SER40

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	1
Details	M-CSA 788

Chain	Residue	Details
C	ASP837	metal ligand
B	ASP483	metal ligand
B	ASP485	metal ligand
B	HIS1085	proton acceptor, proton donor

---