6PSV

Escherichia coli RNA polymerase promoter unwinding intermediate (TpreRPo) with TraR and rpsT P2 promoter

Functional Information from GO Data

Chain	GOid	namespace	contents
G	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed RNA polymerase activity
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006351	biological_process	DNA-templated transcription
G	0006352	biological_process	DNA-templated transcription initiation
G	0006879	biological_process	intracellular iron ion homeostasis
G	0008023	cellular_component	transcription elongation factor complex
G	0009408	biological_process	response to heat
G	0016020	cellular_component	membrane
G	0016740	molecular_function	transferase activity
G	0016779	molecular_function	nucleotidyltransferase activity
G	0031564	biological_process	transcription antitermination
G	0032784	biological_process	regulation of DNA-templated transcription elongation
G	0034062	molecular_function	5'-3' RNA polymerase activity
G	0036460	biological_process	cellular response to cell envelope stress
G	0042128	biological_process	nitrate assimilation
G	0044780	biological_process	bacterial-type flagellum assembly
G	0046983	molecular_function	protein dimerization activity
G	0048870	biological_process	cell motility
G	0071973	biological_process	bacterial-type flagellum-dependent cell motility
G	0090605	biological_process	submerged biofilm formation
G	2000142	biological_process	regulation of DNA-templated transcription initiation
H	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006351	biological_process	DNA-templated transcription
H	0006352	biological_process	DNA-templated transcription initiation
H	0006879	biological_process	intracellular iron ion homeostasis
H	0008023	cellular_component	transcription elongation factor complex
H	0009408	biological_process	response to heat
H	0016020	cellular_component	membrane
H	0016740	molecular_function	transferase activity
H	0016779	molecular_function	nucleotidyltransferase activity
H	0031564	biological_process	transcription antitermination
H	0032784	biological_process	regulation of DNA-templated transcription elongation
H	0034062	molecular_function	5'-3' RNA polymerase activity
H	0036460	biological_process	cellular response to cell envelope stress
H	0042128	biological_process	nitrate assimilation
H	0044780	biological_process	bacterial-type flagellum assembly
H	0046983	molecular_function	protein dimerization activity
H	0048870	biological_process	cell motility
H	0071973	biological_process	bacterial-type flagellum-dependent cell motility
H	0090605	biological_process	submerged biofilm formation
H	2000142	biological_process	regulation of DNA-templated transcription initiation
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 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 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	0001000	molecular_function	bacterial-type RNA polymerase core enzyme binding
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 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	0000976	molecular_function	transcription cis-regulatory region binding
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0003899	molecular_function	DNA-directed RNA polymerase 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	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
M	0000428	cellular_component	DNA-directed RNA polymerase complex
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed RNA polymerase activity
M	0005515	molecular_function	protein binding
M	0005737	cellular_component	cytoplasm
M	0005829	cellular_component	cytosol
M	0006351	biological_process	DNA-templated transcription
M	0006352	biological_process	DNA-templated transcription initiation
M	0006879	biological_process	intracellular iron ion homeostasis
M	0008023	cellular_component	transcription elongation factor complex
M	0009408	biological_process	response to heat
M	0016020	cellular_component	membrane
M	0016740	molecular_function	transferase activity
M	0016779	molecular_function	nucleotidyltransferase activity
M	0031564	biological_process	transcription antitermination
M	0032784	biological_process	regulation of DNA-templated transcription elongation
M	0034062	molecular_function	5'-3' RNA polymerase activity
M	0036460	biological_process	cellular response to cell envelope stress
M	0042128	biological_process	nitrate assimilation
M	0044780	biological_process	bacterial-type flagellum assembly
M	0046983	molecular_function	protein dimerization activity
M	0048870	biological_process	cell motility
M	0071973	biological_process	bacterial-type flagellum-dependent cell motility
M	0090605	biological_process	submerged biofilm formation
M	2000142	biological_process	regulation of DNA-templated transcription initiation
N	0008270	molecular_function	zinc ion binding
N	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN N 101

Chain	Residue
N	CYS37
N	CYS40
N	CYS58
N	CYS61

---

site_id	AC2
Number of Residues	4
Details	binding site for residue 1N7 N 102

Chain	Residue
J	ILE937
J	LEU1243
N	GLN14
N	ASN21

---

site_id	AC3
Number of Residues	7
Details	binding site for residue 1N7 I 1401

Chain	Residue
I	GLN725
I	TYR726
I	ARG731
I	GLN965
I	ILE966
I	ALA969
G	ASP135

---

site_id	AC4
Number of Residues	2
Details	binding site for residue MG J 1501

Chain	Residue
J	ASP462
J	ASP464

---

site_id	AC5
Number of Residues	5
Details	binding site for residue ZN J 1502

Chain	Residue
J	CYS70
J	LEU71
J	CYS72
J	CYS85
J	CYS88

---

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

Chain	Residue
J	CYS814
J	ARG883
J	CYS888
J	ASP889
J	CYS895
J	CYS898

---

site_id	AC7
Number of Residues	2
Details	binding site for residue 1N7 J 1504

Chain	Residue
J	ARG259
L	1N7701

---

site_id	AC8
Number of Residues	6
Details	binding site for residue 1N7 L 701

Chain	Residue
J	LEU255
J	ASP256
J	1N71504
L	ILE511
L	ASP513
L	PHE522

---

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
L	ASP403-VAL416

---

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

Chain	Residue	Details
L	THR572-LEU598

---

site_id	PS01102
Number of Residues	25
Details	ZF_DKSA_1 Prokaryotic dksA C4-type zinc finger. CEaCgnpIpeaRrkifPgvtlCveC

Chain	Residue	Details
N	CYS37-CYS61

---

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

Chain	Residue	Details
I	GLY1063-VAL1075

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Zinc finger: {"description":"dksA C4-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00510","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	Region: {"description":"Required for interaction with Crp at class II promoters"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"ADP-ribosylarginine","evidences":[{"source":"PubMed","id":"4371081","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"21696463","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine; by PatZ","evidences":[{"source":"PubMed","id":"21696463","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01321","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"PubMed","id":"32871103","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4MEX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4MEY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	15
Details	Region: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Site: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

---