4YLO

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0006351	biological_process	DNA-templated transcription
A	0046983	molecular_function	protein dimerization activity
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0006351	biological_process	DNA-templated 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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
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	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006351	biological_process	DNA-templated transcription
D	0006352	biological_process	DNA-templated transcription initiation
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	0006879	biological_process	intracellular iron ion homeostasis
D	0008023	cellular_component	transcription elongation factor complex
D	0008270	molecular_function	zinc ion binding
D	0009408	biological_process	response to heat
D	0016020	cellular_component	membrane
D	0016779	molecular_function	nucleotidyltransferase activity
D	0031564	biological_process	transcription antitermination
D	0032784	biological_process	regulation of DNA-templated transcription elongation
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0036460	biological_process	cellular response to cell envelope stress
D	0042128	biological_process	nitrate assimilation
D	0042793	biological_process	plastid transcription
D	0044780	biological_process	bacterial-type flagellum assembly
D	0046677	biological_process	response to antibiotic
D	0046872	molecular_function	metal ion binding
D	0048870	biological_process	cell motility
D	0071973	biological_process	bacterial-type flagellum-dependent cell motility
D	0090605	biological_process	submerged biofilm formation
D	2000142	biological_process	regulation of DNA-templated transcription initiation
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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0006355	biological_process	regulation of DNA-templated transcription
F	0009408	biological_process	response to heat
F	0010468	biological_process	regulation of gene expression
F	0016987	molecular_function	sigma factor activity
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	1903865	cellular_component	sigma factor antagonist complex
F	2000142	biological_process	regulation of DNA-templated transcription initiation
G	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
G	0006351	biological_process	DNA-templated transcription
G	0046983	molecular_function	protein dimerization activity
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0006351	biological_process	DNA-templated transcription
H	0046983	molecular_function	protein dimerization activity
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	0001057	molecular_function	RNA polymerase IV activity
I	0001058	molecular_function	RNA polymerase V activity
I	0001059	biological_process	transcription by RNA polymerase IV
I	0001060	biological_process	transcription by RNA polymerase V
I	0001066	molecular_function	plastid single subunit type RNA polymerase activity
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0006351	biological_process	DNA-templated transcription
I	0006360	biological_process	transcription by RNA polymerase I
I	0006366	biological_process	transcription by RNA polymerase II
I	0006383	biological_process	transcription by RNA polymerase III
I	0016779	molecular_function	nucleotidyltransferase activity
I	0032549	molecular_function	ribonucleoside binding
I	0034062	molecular_function	5'-3' RNA polymerase activity
I	0042793	biological_process	plastid transcription
J	0000287	molecular_function	magnesium ion binding
J	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001054	molecular_function	RNA polymerase I activity
J	0001055	molecular_function	RNA polymerase II activity
J	0001056	molecular_function	RNA polymerase III activity
J	0001057	molecular_function	RNA polymerase IV activity
J	0001058	molecular_function	RNA polymerase V activity
J	0001059	biological_process	transcription by RNA polymerase IV
J	0001060	biological_process	transcription by RNA polymerase V
J	0001066	molecular_function	plastid single subunit type RNA polymerase activity
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0005515	molecular_function	protein binding
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006351	biological_process	DNA-templated transcription
J	0006352	biological_process	DNA-templated transcription initiation
J	0006360	biological_process	transcription by RNA polymerase I
J	0006366	biological_process	transcription by RNA polymerase II
J	0006383	biological_process	transcription by RNA polymerase III
J	0006879	biological_process	intracellular iron ion homeostasis
J	0008023	cellular_component	transcription elongation factor complex
J	0008270	molecular_function	zinc ion binding
J	0009408	biological_process	response to heat
J	0016020	cellular_component	membrane
J	0016779	molecular_function	nucleotidyltransferase activity
J	0031564	biological_process	transcription antitermination
J	0032784	biological_process	regulation of DNA-templated transcription elongation
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0036460	biological_process	cellular response to cell envelope stress
J	0042128	biological_process	nitrate assimilation
J	0042793	biological_process	plastid transcription
J	0044780	biological_process	bacterial-type flagellum assembly
J	0046677	biological_process	response to antibiotic
J	0046872	molecular_function	metal ion binding
J	0048870	biological_process	cell motility
J	0071973	biological_process	bacterial-type flagellum-dependent cell motility
J	0090605	biological_process	submerged biofilm formation
J	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	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
L	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006351	biological_process	DNA-templated transcription
L	0006352	biological_process	DNA-templated transcription initiation
L	0006355	biological_process	regulation of DNA-templated transcription
L	0009408	biological_process	response to heat
L	0010468	biological_process	regulation of gene expression
L	0016987	molecular_function	sigma factor activity
L	0045892	biological_process	negative regulation of DNA-templated transcription
L	1903865	cellular_component	sigma factor antagonist complex
L	2000142	biological_process	regulation of DNA-templated transcription initiation
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	0046983	molecular_function	protein dimerization activity
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
N	0006351	biological_process	DNA-templated transcription
N	0046983	molecular_function	protein dimerization activity
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	0032549	molecular_function	ribonucleoside binding
O	0034062	molecular_function	5'-3' RNA polymerase activity
O	0042793	biological_process	plastid transcription
P	0000287	molecular_function	magnesium ion binding
P	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
P	0000428	cellular_component	DNA-directed RNA polymerase complex
P	0001054	molecular_function	RNA polymerase I activity
P	0001055	molecular_function	RNA polymerase II activity
P	0001056	molecular_function	RNA polymerase III activity
P	0001057	molecular_function	RNA polymerase IV activity
P	0001058	molecular_function	RNA polymerase V activity
P	0001059	biological_process	transcription by RNA polymerase IV
P	0001060	biological_process	transcription by RNA polymerase V
P	0001066	molecular_function	plastid single subunit type RNA polymerase activity
P	0003677	molecular_function	DNA binding
P	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
P	0005515	molecular_function	protein binding
P	0005737	cellular_component	cytoplasm
P	0005829	cellular_component	cytosol
P	0006351	biological_process	DNA-templated transcription
P	0006352	biological_process	DNA-templated transcription initiation
P	0006360	biological_process	transcription by RNA polymerase I
P	0006366	biological_process	transcription by RNA polymerase II
P	0006383	biological_process	transcription by RNA polymerase III
P	0006879	biological_process	intracellular iron ion homeostasis
P	0008023	cellular_component	transcription elongation factor complex
P	0008270	molecular_function	zinc ion binding
P	0009408	biological_process	response to heat
P	0016020	cellular_component	membrane
P	0016779	molecular_function	nucleotidyltransferase activity
P	0031564	biological_process	transcription antitermination
P	0032784	biological_process	regulation of DNA-templated transcription elongation
P	0034062	molecular_function	5'-3' RNA polymerase activity
P	0036460	biological_process	cellular response to cell envelope stress
P	0042128	biological_process	nitrate assimilation
P	0042793	biological_process	plastid transcription
P	0044780	biological_process	bacterial-type flagellum assembly
P	0046677	biological_process	response to antibiotic
P	0046872	molecular_function	metal ion binding
P	0048870	biological_process	cell motility
P	0071973	biological_process	bacterial-type flagellum-dependent cell motility
P	0090605	biological_process	submerged biofilm formation
P	2000142	biological_process	regulation of DNA-templated transcription initiation
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0001054	molecular_function	RNA polymerase I activity
Q	0001055	molecular_function	RNA polymerase II activity
Q	0001056	molecular_function	RNA polymerase III activity
Q	0001057	molecular_function	RNA polymerase IV activity
Q	0001058	molecular_function	RNA polymerase V activity
Q	0001059	biological_process	transcription by RNA polymerase IV
Q	0001060	biological_process	transcription by RNA polymerase V
Q	0001066	molecular_function	plastid single subunit type RNA polymerase activity
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
Q	0006351	biological_process	DNA-templated transcription
Q	0006360	biological_process	transcription by RNA polymerase I
Q	0006366	biological_process	transcription by RNA polymerase II
Q	0006383	biological_process	transcription by RNA polymerase III
Q	0016779	molecular_function	nucleotidyltransferase activity
Q	0034062	molecular_function	5'-3' RNA polymerase activity
Q	0042793	biological_process	plastid transcription
R	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
R	0003677	molecular_function	DNA binding
R	0003700	molecular_function	DNA-binding transcription factor activity
R	0005515	molecular_function	protein binding
R	0005737	cellular_component	cytoplasm
R	0005829	cellular_component	cytosol
R	0006351	biological_process	DNA-templated transcription
R	0006352	biological_process	DNA-templated transcription initiation
R	0006355	biological_process	regulation of DNA-templated transcription
R	0009408	biological_process	response to heat
R	0010468	biological_process	regulation of gene expression
R	0016987	molecular_function	sigma factor activity
R	0045892	biological_process	negative regulation of DNA-templated transcription
R	1903865	cellular_component	sigma factor antagonist complex
R	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 C 1401

Chain	Residue
C	ARG678
C	ASP814
C	ARG1106
D	ASP462

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN D 1501

Chain	Residue
D	CYS70
D	CYS72
D	CYS85
D	CYS88

---

site_id	AC3
Number of Residues	5
Details	binding site for residue ZN D 1502

Chain	Residue
D	ARG883
D	CYS888
D	CYS895
D	CYS898
D	CYS814

---

site_id	AC4
Number of Residues	5
Details	binding site for residue ZN J 1501

Chain	Residue
J	CYS70
J	CYS72
J	LYS74
J	CYS85
J	CYS88

---

site_id	AC5
Number of Residues	6
Details	binding site for residue ZN J 1502

Chain	Residue
J	CYS814
J	ARG883
J	CYS888
J	THR890
J	CYS895
J	CYS898

---

site_id	AC6
Number of Residues	4
Details	binding site for residue MG J 1503

Chain	Residue
6	G15
J	ASP460
J	ASP462
J	ASP464

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN P 1501

Chain	Residue
P	CYS70
P	CYS72
P	CYS85
P	CYS88

---

site_id	AC8
Number of Residues	5
Details	binding site for residue ZN P 1502

Chain	Residue
P	CYS814
P	ARG883
P	CYS888
P	CYS895
P	CYS898

---

site_id	AC9
Number of Residues	5
Details	binding site for residue MG P 1503

Chain	Residue
9	G15
9	U16
P	ASP460
P	ASP462
P	ASP464

---

site_id	AD1
Number of Residues	12
Details	binding site for nucleotide GTP 3 13

Chain	Residue
2	DC16
2	DG17
3	G15
C	GLN513
C	ARG529
C	PRO564
C	ASN568
C	ILE572
C	ASN684
C	GLN688
C	LYS1065
D	GLY463

---

site_id	AD2
Number of Residues	10
Details	binding site for nucleotide GTP 6 13

Chain	Residue
5	DT15
5	DC16
5	DG17
6	G15
I	ARG529
I	PRO564
I	ASN568
I	GLN688
I	LYS1065
J	GLY463

---

site_id	AD3
Number of Residues	9
Details	binding site for nucleotide GTP 9 13

Chain	Residue
8	DT15
8	DC16
8	DG17
9	G15
O	PRO564
O	ASN568
O	GLN688
O	LYS1065
P	GLY463

---

Functional Information from PROSITE/UniProt

site_id	PS00715
Number of Residues	14
Details	SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV

Chain	Residue	Details
F	ASP403-VAL416

---

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

Chain	Residue	Details
F	THR572-LEU598

---

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

Chain	Residue	Details
C	GLY1063-VAL1075

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	57
Details	DNA_BIND: H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963

Chain	Residue	Details
F	LEU573-ALA592
D	CYS895
D	CYS898
J	CYS70
J	CYS72
J	CYS85
J	CYS88
J	ASP460
J	ASP462
J	ASP464
J	CYS814
L	LEU573-ALA592
J	CYS888
J	CYS895
J	CYS898
P	CYS70
P	CYS72
P	CYS85
P	CYS88
P	ASP460
P	ASP462
P	ASP464
R	LEU573-ALA592
P	CYS814
P	CYS888
P	CYS895
P	CYS898
D	CYS88
D	ASP460
D	ASP462
D	ASP464
D	CYS814
D	CYS888

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	SITE: Interaction with anti-sigma factors

Chain	Residue	Details
F	ARG562
L	ARG562
R	ARG562

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000255|HAMAP-Rule:MF_01322, ECO:0000269|PubMed:18723842

Chain	Residue	Details
D	LYS983
J	LYS983
P	LYS983

---