5D4E

Crystal structure of Thermus thermophilus product complex for transcription initiation with 3'-dephosphate-CoA and CTP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0001054	molecular_function	RNA polymerase I activity
A	0001055	molecular_function	RNA polymerase II activity
A	0001056	molecular_function	RNA polymerase III activity
A	0001057	molecular_function	RNA polymerase IV activity
A	0001058	molecular_function	RNA polymerase V activity
A	0001059	biological_process	transcription by RNA polymerase IV
A	0001060	biological_process	transcription by RNA polymerase V
A	0001066	molecular_function	plastid single subunit type RNA polymerase activity
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0006360	biological_process	transcription by RNA polymerase I
A	0006366	biological_process	transcription by RNA polymerase II
A	0006383	biological_process	transcription by RNA polymerase III
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042793	biological_process	plastid transcription
A	0046983	molecular_function	protein dimerization activity
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001054	molecular_function	RNA polymerase I activity
B	0001055	molecular_function	RNA polymerase II activity
B	0001056	molecular_function	RNA polymerase III activity
B	0001057	molecular_function	RNA polymerase IV activity
B	0001058	molecular_function	RNA polymerase V activity
B	0001059	biological_process	transcription by RNA polymerase IV
B	0001060	biological_process	transcription by RNA polymerase V
B	0001066	molecular_function	plastid single subunit type RNA polymerase activity
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0006360	biological_process	transcription by RNA polymerase I
B	0006366	biological_process	transcription by RNA polymerase II
B	0006383	biological_process	transcription by RNA polymerase III
B	0016779	molecular_function	nucleotidyltransferase activity
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0042793	biological_process	plastid transcription
B	0046983	molecular_function	protein dimerization activity
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001054	molecular_function	RNA polymerase I activity
C	0001055	molecular_function	RNA polymerase II activity
C	0001056	molecular_function	RNA polymerase III activity
C	0001057	molecular_function	RNA polymerase IV activity
C	0001058	molecular_function	RNA polymerase V activity
C	0001059	biological_process	transcription by RNA polymerase IV
C	0001060	biological_process	transcription by RNA polymerase V
C	0001066	molecular_function	plastid single subunit type RNA polymerase activity
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0006351	biological_process	DNA-templated transcription
C	0006360	biological_process	transcription by RNA polymerase I
C	0006366	biological_process	transcription by RNA polymerase II
C	0006383	biological_process	transcription by RNA polymerase III
C	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
C	0042793	biological_process	plastid transcription
D	0000287	molecular_function	magnesium ion binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0001054	molecular_function	RNA polymerase I activity
D	0001055	molecular_function	RNA polymerase II activity
D	0001056	molecular_function	RNA polymerase III activity
D	0001057	molecular_function	RNA polymerase IV activity
D	0001058	molecular_function	RNA polymerase V activity
D	0001059	biological_process	transcription by RNA polymerase IV
D	0001060	biological_process	transcription by RNA polymerase V
D	0001066	molecular_function	plastid single subunit type RNA polymerase activity
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
D	0005515	molecular_function	protein binding
D	0006351	biological_process	DNA-templated transcription
D	0006360	biological_process	transcription by RNA polymerase I
D	0006366	biological_process	transcription by RNA polymerase II
D	0006383	biological_process	transcription by RNA polymerase III
D	0008270	molecular_function	zinc ion binding
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0042793	biological_process	plastid transcription
D	0046872	molecular_function	metal ion binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0001054	molecular_function	RNA polymerase I activity
E	0001055	molecular_function	RNA polymerase II activity
E	0001056	molecular_function	RNA polymerase III activity
E	0001057	molecular_function	RNA polymerase IV activity
E	0001058	molecular_function	RNA polymerase V activity
E	0001059	biological_process	transcription by RNA polymerase IV
E	0001060	biological_process	transcription by RNA polymerase V
E	0001066	molecular_function	plastid single subunit type RNA polymerase activity
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0006351	biological_process	DNA-templated transcription
E	0006360	biological_process	transcription by RNA polymerase I
E	0006366	biological_process	transcription by RNA polymerase II
E	0006383	biological_process	transcription by RNA polymerase III
E	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
E	0042793	biological_process	plastid transcription
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0005737	cellular_component	cytoplasm
F	0006352	biological_process	DNA-templated transcription initiation
F	0006355	biological_process	regulation of DNA-templated transcription
F	0010468	biological_process	regulation of gene expression
F	0016987	molecular_function	sigma factor activity
F	0046872	molecular_function	metal ion binding
F	2000142	biological_process	regulation of DNA-templated transcription initiation
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	0001057	molecular_function	RNA polymerase IV activity
K	0001058	molecular_function	RNA polymerase V activity
K	0001059	biological_process	transcription by RNA polymerase IV
K	0001060	biological_process	transcription by RNA polymerase V
K	0001066	molecular_function	plastid single subunit type RNA polymerase activity
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0005515	molecular_function	protein binding
K	0005737	cellular_component	cytoplasm
K	0006351	biological_process	DNA-templated transcription
K	0006360	biological_process	transcription by RNA polymerase I
K	0006366	biological_process	transcription by RNA polymerase II
K	0006383	biological_process	transcription by RNA polymerase III
K	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
K	0042793	biological_process	plastid transcription
K	0046983	molecular_function	protein dimerization activity
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001054	molecular_function	RNA polymerase I activity
L	0001055	molecular_function	RNA polymerase II activity
L	0001056	molecular_function	RNA polymerase III activity
L	0001057	molecular_function	RNA polymerase IV activity
L	0001058	molecular_function	RNA polymerase V activity
L	0001059	biological_process	transcription by RNA polymerase IV
L	0001060	biological_process	transcription by RNA polymerase V
L	0001066	molecular_function	plastid single subunit type RNA polymerase activity
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0006351	biological_process	DNA-templated transcription
L	0006360	biological_process	transcription by RNA polymerase I
L	0006366	biological_process	transcription by RNA polymerase II
L	0006383	biological_process	transcription by RNA polymerase III
L	0016779	molecular_function	nucleotidyltransferase activity
L	0034062	molecular_function	5'-3' RNA polymerase activity
L	0042793	biological_process	plastid 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	0001057	molecular_function	RNA polymerase IV activity
M	0001058	molecular_function	RNA polymerase V activity
M	0001059	biological_process	transcription by RNA polymerase IV
M	0001060	biological_process	transcription by RNA polymerase V
M	0001066	molecular_function	plastid single subunit type RNA polymerase activity
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
M	0006351	biological_process	DNA-templated transcription
M	0006360	biological_process	transcription by RNA polymerase I
M	0006366	biological_process	transcription by RNA polymerase II
M	0006383	biological_process	transcription by RNA polymerase III
M	0016779	molecular_function	nucleotidyltransferase activity
M	0032549	molecular_function	ribonucleoside binding
M	0034062	molecular_function	5'-3' RNA polymerase activity
M	0042793	biological_process	plastid transcription
N	0000287	molecular_function	magnesium ion binding
N	0000428	cellular_component	DNA-directed RNA polymerase complex
N	0001054	molecular_function	RNA polymerase I activity
N	0001055	molecular_function	RNA polymerase II activity
N	0001056	molecular_function	RNA polymerase III activity
N	0001057	molecular_function	RNA polymerase IV activity
N	0001058	molecular_function	RNA polymerase V activity
N	0001059	biological_process	transcription by RNA polymerase IV
N	0001060	biological_process	transcription by RNA polymerase V
N	0001066	molecular_function	plastid single subunit type RNA polymerase activity
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
N	0005515	molecular_function	protein binding
N	0006351	biological_process	DNA-templated transcription
N	0006360	biological_process	transcription by RNA polymerase I
N	0006366	biological_process	transcription by RNA polymerase II
N	0006383	biological_process	transcription by RNA polymerase III
N	0008270	molecular_function	zinc ion binding
N	0016779	molecular_function	nucleotidyltransferase activity
N	0034062	molecular_function	5'-3' RNA polymerase activity
N	0042793	biological_process	plastid transcription
N	0046872	molecular_function	metal ion binding
O	0000428	cellular_component	DNA-directed RNA polymerase complex
O	0001054	molecular_function	RNA polymerase I activity
O	0001055	molecular_function	RNA polymerase II activity
O	0001056	molecular_function	RNA polymerase III activity
O	0001057	molecular_function	RNA polymerase IV activity
O	0001058	molecular_function	RNA polymerase V activity
O	0001059	biological_process	transcription by RNA polymerase IV
O	0001060	biological_process	transcription by RNA polymerase V
O	0001066	molecular_function	plastid single subunit type RNA polymerase activity
O	0003677	molecular_function	DNA binding
O	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
O	0006351	biological_process	DNA-templated transcription
O	0006360	biological_process	transcription by RNA polymerase I
O	0006366	biological_process	transcription by RNA polymerase II
O	0006383	biological_process	transcription by RNA polymerase III
O	0016779	molecular_function	nucleotidyltransferase activity
O	0034062	molecular_function	5'-3' RNA polymerase activity
O	0042793	biological_process	plastid transcription
P	0003677	molecular_function	DNA binding
P	0003700	molecular_function	DNA-binding transcription factor activity
P	0005737	cellular_component	cytoplasm
P	0006352	biological_process	DNA-templated transcription initiation
P	0006355	biological_process	regulation of DNA-templated transcription
P	0010468	biological_process	regulation of gene expression
P	0016987	molecular_function	sigma factor activity
P	0046872	molecular_function	metal ion binding
P	2000142	biological_process	regulation of DNA-templated transcription initiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue MG B 2001

Chain	Residue
B	ARG30
B	ASP183
B	ASP191
B	ASP193

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN D 2001

Chain	Residue
D	CYS1112
D	CYS1194
D	CYS1201
D	CYS1204

---

site_id	AC3
Number of Residues	5
Details	binding site for residue ZN D 2002

Chain	Residue
D	CYS60
D	LYS62
D	CYS73
D	CYS76
D	CYS58

---

site_id	AC4
Number of Residues	4
Details	binding site for residue MG D 2003

Chain	Residue
D	ASP739
D	ASP741
D	ASP743
D	C5P2005

---

site_id	AC5
Number of Residues	2
Details	binding site for residue MG D 2004

Chain	Residue
B	ASP168
D	LYS840

---

site_id	AC6
Number of Residues	4
Details	binding site for residue DPO D 2006

Chain	Residue
C	ARG879
D	ASP739
D	ARG1029
D	MG2007

---

site_id	AC7
Number of Residues	3
Details	binding site for residue MG D 2007

Chain	Residue
C	ARG879
D	ASP739
D	DPO2006

---

site_id	AC8
Number of Residues	3
Details	binding site for residue MG F 2001

Chain	Residue
F	ALA292
F	GLY296
F	TRP299

---

site_id	AC9
Number of Residues	2
Details	binding site for residue MG L 1601

Chain	Residue
L	ASP168
N	LYS840

---

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN N 1601

Chain	Residue
N	CYS1112
N	CYS1194
N	CYS1201
N	CYS1204

---

site_id	AD2
Number of Residues	4
Details	binding site for residue ZN N 1602

Chain	Residue
N	CYS58
N	CYS60
N	CYS73
N	CYS76

---

site_id	AD3
Number of Residues	4
Details	binding site for residue MG N 1603

Chain	Residue
N	ASP739
N	ASP741
N	ASP743
N	C5P1604

---

site_id	AD4
Number of Residues	5
Details	binding site for residue DPO N 1605

Chain	Residue
M	ARG879
N	ASP739
N	ARG1029
N	MG1606
N	HOH2140

---

site_id	AD5
Number of Residues	4
Details	binding site for residue MG N 1606

Chain	Residue
M	GLU685
M	HOH1216
N	ASP739
N	DPO1605

---

site_id	AD6
Number of Residues	3
Details	binding site for residue MG P 2001

Chain	Residue
P	ALA292
P	GLY296
P	TRP299

---

site_id	AD7
Number of Residues	12
Details	binding site for Di-nucleotide C D 2005 and COD D 2008

Chain	Residue
C	GLN567
C	LYS838
C	LYS846
C	HIS999
D	ARG704
D	ASP741
D	ASP743
D	MG2003
D	HOH2136
G	DG15
G	DT16
G	DA17

---

site_id	AD8
Number of Residues	12
Details	binding site for Di-nucleotide C N 1605 and COD N 1608

Chain	Residue
M	GLN567
M	LYS838
M	LYS846
M	TYR998
M	HIS999
N	ARG704
N	ASP741
N	ASP743
N	MG1603
R	DG15
R	DT16
R	DA17

---

Functional Information from PROSITE/UniProt

site_id	PS00716
Number of Residues	27
Details	SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL

Chain	Residue	Details
F	THR382-LEU408

---

site_id	PS00867
Number of Residues	8
Details	CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL

Chain	Residue	Details
F	LEU187-LEU194

---

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

Chain	Residue	Details
C	GLY836-VAL848

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	38
Details	DNA_BIND: H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963

Chain	Residue	Details
F	LEU383-ASN402
D	CYS1201
D	CYS1204
N	CYS58
N	CYS60
N	CYS73
N	CYS76
N	ASP739
N	ASP741
N	ASP743
N	CYS1112
P	LEU383-ASN402
N	CYS1194
N	CYS1201
N	CYS1204
D	CYS73
D	CYS76
D	ASP739
D	ASP741
D	ASP743
D	CYS1112
D	CYS1194

---