4YLP

E. coli Transcription Initiation Complex - 16-bp spacer and 5-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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006351	biological_process	DNA-templated transcription
C	0006352	biological_process	DNA-templated transcription initiation
C	0006879	biological_process	intracellular iron ion homeostasis
C	0008023	cellular_component	transcription elongation factor complex
C	0009408	biological_process	response to heat
C	0016020	cellular_component	membrane
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0031564	biological_process	transcription antitermination
C	0032549	molecular_function	ribonucleoside binding
C	0032784	biological_process	regulation of DNA-templated transcription elongation
C	0034062	molecular_function	5'-3' RNA polymerase activity
C	0036460	biological_process	cellular response to cell envelope stress
C	0042128	biological_process	nitrate assimilation
C	0044780	biological_process	bacterial-type flagellum assembly
C	0046677	biological_process	response to antibiotic
C	0048870	biological_process	cell motility
C	0071973	biological_process	bacterial-type flagellum-dependent cell motility
C	0090605	biological_process	submerged biofilm formation
C	2000142	biological_process	regulation of DNA-templated transcription initiation
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	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	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	0016740	molecular_function	transferase activity
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	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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0005829	cellular_component	cytosol
E	0006351	biological_process	DNA-templated transcription
E	0006352	biological_process	DNA-templated transcription initiation
E	0006879	biological_process	intracellular iron ion homeostasis
E	0008023	cellular_component	transcription elongation factor complex
E	0009408	biological_process	response to heat
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0030880	cellular_component	RNA polymerase complex
E	0031564	biological_process	transcription antitermination
E	0032784	biological_process	regulation of DNA-templated transcription elongation
E	0034062	molecular_function	5'-3' RNA polymerase activity
E	0036460	biological_process	cellular response to cell envelope stress
E	0042128	biological_process	nitrate assimilation
E	0044780	biological_process	bacterial-type flagellum assembly
E	0048870	biological_process	cell motility
E	0065003	biological_process	protein-containing complex assembly
E	0071973	biological_process	bacterial-type flagellum-dependent cell motility
E	0090605	biological_process	submerged biofilm formation
E	2000142	biological_process	regulation of DNA-templated transcription initiation
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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0005515	molecular_function	protein binding
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006351	biological_process	DNA-templated transcription
I	0006352	biological_process	DNA-templated transcription initiation
I	0006879	biological_process	intracellular iron ion homeostasis
I	0008023	cellular_component	transcription elongation factor complex
I	0009408	biological_process	response to heat
I	0016020	cellular_component	membrane
I	0016740	molecular_function	transferase activity
I	0016779	molecular_function	nucleotidyltransferase activity
I	0031564	biological_process	transcription antitermination
I	0032549	molecular_function	ribonucleoside binding
I	0032784	biological_process	regulation of DNA-templated transcription elongation
I	0034062	molecular_function	5'-3' RNA polymerase activity
I	0036460	biological_process	cellular response to cell envelope stress
I	0042128	biological_process	nitrate assimilation
I	0044780	biological_process	bacterial-type flagellum assembly
I	0046677	biological_process	response to antibiotic
I	0048870	biological_process	cell motility
I	0071973	biological_process	bacterial-type flagellum-dependent cell motility
I	0090605	biological_process	submerged biofilm formation
I	2000142	biological_process	regulation of DNA-templated transcription initiation
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	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	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	0016740	molecular_function	transferase activity
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	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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0005829	cellular_component	cytosol
K	0006351	biological_process	DNA-templated transcription
K	0006352	biological_process	DNA-templated transcription initiation
K	0006879	biological_process	intracellular iron ion homeostasis
K	0008023	cellular_component	transcription elongation factor complex
K	0009408	biological_process	response to heat
K	0016740	molecular_function	transferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0030880	cellular_component	RNA polymerase complex
K	0031564	biological_process	transcription antitermination
K	0032784	biological_process	regulation of DNA-templated transcription elongation
K	0034062	molecular_function	5'-3' RNA polymerase activity
K	0036460	biological_process	cellular response to cell envelope stress
K	0042128	biological_process	nitrate assimilation
K	0044780	biological_process	bacterial-type flagellum assembly
K	0048870	biological_process	cell motility
K	0065003	biological_process	protein-containing complex assembly
K	0071973	biological_process	bacterial-type flagellum-dependent cell motility
K	0090605	biological_process	submerged biofilm formation
K	2000142	biological_process	regulation of DNA-templated transcription initiation
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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
O	0000428	cellular_component	DNA-directed RNA polymerase complex
O	0003677	molecular_function	DNA binding
O	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
O	0005515	molecular_function	protein binding
O	0005737	cellular_component	cytoplasm
O	0005829	cellular_component	cytosol
O	0006351	biological_process	DNA-templated transcription
O	0006352	biological_process	DNA-templated transcription initiation
O	0006879	biological_process	intracellular iron ion homeostasis
O	0008023	cellular_component	transcription elongation factor complex
O	0009408	biological_process	response to heat
O	0016020	cellular_component	membrane
O	0016740	molecular_function	transferase activity
O	0016779	molecular_function	nucleotidyltransferase activity
O	0031564	biological_process	transcription antitermination
O	0032549	molecular_function	ribonucleoside binding
O	0032784	biological_process	regulation of DNA-templated transcription elongation
O	0034062	molecular_function	5'-3' RNA polymerase activity
O	0036460	biological_process	cellular response to cell envelope stress
O	0042128	biological_process	nitrate assimilation
O	0044780	biological_process	bacterial-type flagellum assembly
O	0046677	biological_process	response to antibiotic
O	0048870	biological_process	cell motility
O	0071973	biological_process	bacterial-type flagellum-dependent cell motility
O	0090605	biological_process	submerged biofilm formation
O	2000142	biological_process	regulation of DNA-templated transcription initiation
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	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	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	0016740	molecular_function	transferase activity
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	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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
Q	0005829	cellular_component	cytosol
Q	0006351	biological_process	DNA-templated transcription
Q	0006352	biological_process	DNA-templated transcription initiation
Q	0006879	biological_process	intracellular iron ion homeostasis
Q	0008023	cellular_component	transcription elongation factor complex
Q	0009408	biological_process	response to heat
Q	0016740	molecular_function	transferase activity
Q	0016779	molecular_function	nucleotidyltransferase activity
Q	0030880	cellular_component	RNA polymerase complex
Q	0031564	biological_process	transcription antitermination
Q	0032784	biological_process	regulation of DNA-templated transcription elongation
Q	0034062	molecular_function	5'-3' RNA polymerase activity
Q	0036460	biological_process	cellular response to cell envelope stress
Q	0042128	biological_process	nitrate assimilation
Q	0044780	biological_process	bacterial-type flagellum assembly
Q	0048870	biological_process	cell motility
Q	0065003	biological_process	protein-containing complex assembly
Q	0071973	biological_process	bacterial-type flagellum-dependent cell motility
Q	0090605	biological_process	submerged biofilm formation
Q	2000142	biological_process	regulation of DNA-templated transcription initiation
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 ZN D 1501

Chain	Residue
D	CYS70
D	CYS72
D	CYS85
D	CYS88

---

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN D 1502

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

---

site_id	AC3
Number of Residues	5
Details	binding site for residue MG D 1503

Chain	Residue
3	U16
3	C17
D	ASP460
D	ASP462
D	ASP464

---

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

Chain	Residue
J	CYS70
J	CYS72
J	GLY73
J	CYS85
J	CYS88

---

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

Chain	Residue
J	CYS814
J	THR816
J	ARG883
J	CYS888
J	CYS895
J	CYS898

---

site_id	AC6
Number of Residues	6
Details	binding site for residue MG J 1503

Chain	Residue
6	U16
6	C17
I	LYS1073
J	ASP460
J	ASP462
J	ASP464

---

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN P 1501

Chain	Residue
P	CYS70
P	CYS72
P	LYS74
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	4
Details	binding site for residue MG P 1503

Chain	Residue
9	C17
O	ARG1106
P	ASP460
P	ASP462

---

site_id	AD1
Number of Residues	11
Details	binding site for nucleotide GTP 3 13

Chain	Residue
2	DT15
2	DC16
2	DG17
3	G15
C	ARG529
C	ASN568
C	ILE572
C	ARG687
C	GLN688
C	HIS1237
F	ASP514

---

site_id	AD2
Number of Residues	11
Details	binding site for nucleotide GTP 6 13

Chain	Residue
5	DC16
5	DG17
6	G15
I	GLN510
I	ARG529
I	ARG540
I	PRO564
I	ARG687
I	GLN688
I	HIS1237
L	ASP514

---

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

Chain	Residue
8	DC16
9	G15
O	GLN513
O	ARG529
O	ARG540
O	PRO564
O	ASN568
R	ASP513
R	ASP514

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	GLY1063-VAL1075

---

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

---

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

---