Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3HKZ

The X-ray crystal structure of RNA polymerase from Archaea

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0008270	molecular_function	zinc ion binding
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0008270	molecular_function	zinc ion binding
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
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	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0005737	cellular_component	cytoplasm
C	0006351	biological_process	DNA-templated transcription
C	0016779	molecular_function	nucleotidyltransferase activity
C	0034062	molecular_function	5'-3' RNA polymerase activity
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	0006351	biological_process	DNA-templated transcription
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0046872	molecular_function	metal ion binding
D	0046983	molecular_function	protein dimerization activity
D	0051536	molecular_function	iron-sulfur cluster binding
D	0051538	molecular_function	3 iron, 4 sulfur cluster binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0005737	cellular_component	cytoplasm
E	0006351	biological_process	DNA-templated transcription
E	0006352	biological_process	DNA-templated transcription initiation
E	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
F	0000166	molecular_function	nucleotide binding
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
F	0005737	cellular_component	cytoplasm
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0016779	molecular_function	nucleotidyltransferase activity
F	0030880	cellular_component	RNA polymerase complex
F	0034062	molecular_function	5'-3' RNA polymerase activity
F	0044237	biological_process	cellular metabolic process
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
G	0005737	cellular_component	cytoplasm
G	0006351	biological_process	DNA-templated transcription
G	0016779	molecular_function	nucleotidyltransferase activity
G	0034062	molecular_function	5'-3' RNA polymerase activity
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0005737	cellular_component	cytoplasm
H	0006351	biological_process	DNA-templated transcription
H	0016779	molecular_function	nucleotidyltransferase activity
H	0034062	molecular_function	5'-3' RNA polymerase activity
I	0000287	molecular_function	magnesium ion binding
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	0006351	biological_process	DNA-templated transcription
I	0008270	molecular_function	zinc ion binding
I	0016779	molecular_function	nucleotidyltransferase activity
I	0034062	molecular_function	5'-3' RNA polymerase activity
I	0046872	molecular_function	metal ion binding
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	0005737	cellular_component	cytoplasm
J	0006351	biological_process	DNA-templated transcription
J	0008270	molecular_function	zinc ion binding
J	0016779	molecular_function	nucleotidyltransferase activity
J	0032549	molecular_function	ribonucleoside binding
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0046872	molecular_function	metal ion binding
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	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
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	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
K	0042797	biological_process	tRNA transcription by RNA polymerase III
L	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0016779	molecular_function	nucleotidyltransferase activity
L	0034062	molecular_function	5'-3' RNA polymerase activity
L	0046983	molecular_function	protein dimerization activity
M	0000428	cellular_component	DNA-directed RNA polymerase complex
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
M	0005737	cellular_component	cytoplasm
M	0006351	biological_process	DNA-templated transcription
M	0016779	molecular_function	nucleotidyltransferase activity
M	0034062	molecular_function	5'-3' RNA polymerase activity
N	0000428	cellular_component	DNA-directed RNA polymerase complex
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
N	0005737	cellular_component	cytoplasm
N	0006351	biological_process	DNA-templated transcription
N	0008270	molecular_function	zinc ion binding
N	0016779	molecular_function	nucleotidyltransferase activity
N	0034062	molecular_function	5'-3' RNA polymerase activity
N	0046872	molecular_function	metal ion binding
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	0006351	biological_process	DNA-templated transcription
O	0016779	molecular_function	nucleotidyltransferase activity
O	0034062	molecular_function	5'-3' RNA polymerase activity
O	0046872	molecular_function	metal ion binding
O	0046983	molecular_function	protein dimerization activity
O	0051536	molecular_function	iron-sulfur cluster binding
O	0051538	molecular_function	3 iron, 4 sulfur cluster binding
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	0005737	cellular_component	cytoplasm
P	0006351	biological_process	DNA-templated transcription
P	0008270	molecular_function	zinc ion binding
P	0016779	molecular_function	nucleotidyltransferase activity
P	0034062	molecular_function	5'-3' RNA polymerase activity
P	0046872	molecular_function	metal ion binding
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0003676	molecular_function	nucleic acid binding
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
Q	0005737	cellular_component	cytoplasm
Q	0006351	biological_process	DNA-templated transcription
Q	0006352	biological_process	DNA-templated transcription initiation
Q	0016779	molecular_function	nucleotidyltransferase activity
Q	0034062	molecular_function	5'-3' RNA polymerase activity
R	0000166	molecular_function	nucleotide binding
R	0000428	cellular_component	DNA-directed RNA polymerase complex
R	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
R	0005737	cellular_component	cytoplasm
R	0006351	biological_process	DNA-templated transcription
R	0006352	biological_process	DNA-templated transcription initiation
R	0016779	molecular_function	nucleotidyltransferase activity
R	0030880	cellular_component	RNA polymerase complex
R	0034062	molecular_function	5'-3' RNA polymerase activity
R	0044237	biological_process	cellular metabolic process
S	0000428	cellular_component	DNA-directed RNA polymerase complex
S	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
S	0005737	cellular_component	cytoplasm
S	0006351	biological_process	DNA-templated transcription
S	0016779	molecular_function	nucleotidyltransferase activity
S	0034062	molecular_function	5'-3' RNA polymerase activity
T	0000428	cellular_component	DNA-directed RNA polymerase complex
T	0003677	molecular_function	DNA binding
T	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
T	0005737	cellular_component	cytoplasm
T	0006351	biological_process	DNA-templated transcription
T	0016779	molecular_function	nucleotidyltransferase activity
T	0034062	molecular_function	5'-3' RNA polymerase activity
U	0000428	cellular_component	DNA-directed RNA polymerase complex
U	0001054	molecular_function	RNA polymerase I activity
U	0001055	molecular_function	RNA polymerase II activity
U	0001056	molecular_function	RNA polymerase III activity
U	0003677	molecular_function	DNA binding
U	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
U	0005737	cellular_component	cytoplasm
U	0006351	biological_process	DNA-templated transcription
U	0006360	biological_process	transcription by RNA polymerase I
U	0006366	biological_process	transcription by RNA polymerase II
U	0016779	molecular_function	nucleotidyltransferase activity
U	0034062	molecular_function	5'-3' RNA polymerase activity
U	0042797	biological_process	tRNA transcription by RNA polymerase III
V	0000428	cellular_component	DNA-directed RNA polymerase complex
V	0003677	molecular_function	DNA binding
V	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
V	0005515	molecular_function	protein binding
V	0005737	cellular_component	cytoplasm
V	0006351	biological_process	DNA-templated transcription
V	0016779	molecular_function	nucleotidyltransferase activity
V	0034062	molecular_function	5'-3' RNA polymerase activity
V	0046983	molecular_function	protein dimerization activity
W	0000428	cellular_component	DNA-directed RNA polymerase complex
W	0003677	molecular_function	DNA binding
W	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
W	0005737	cellular_component	cytoplasm
W	0006351	biological_process	DNA-templated transcription
W	0008270	molecular_function	zinc ion binding
W	0016779	molecular_function	nucleotidyltransferase activity
W	0034062	molecular_function	5'-3' RNA polymerase activity
W	0046872	molecular_function	metal ion binding
X	0000428	cellular_component	DNA-directed RNA polymerase complex
X	0003677	molecular_function	DNA binding
X	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
X	0005737	cellular_component	cytoplasm
X	0006351	biological_process	DNA-templated transcription
X	0008270	molecular_function	zinc ion binding
X	0016779	molecular_function	nucleotidyltransferase activity
X	0034062	molecular_function	5'-3' RNA polymerase activity
X	0046872	molecular_function	metal ion binding
Y	0000428	cellular_component	DNA-directed RNA polymerase complex
Y	0003677	molecular_function	DNA binding
Y	0005737	cellular_component	cytoplasm
Y	0016779	molecular_function	nucleotidyltransferase activity
Z	0000428	cellular_component	DNA-directed RNA polymerase complex
Z	0003677	molecular_function	DNA binding
Z	0005737	cellular_component	cytoplasm
Z	0016779	molecular_function	nucleotidyltransferase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 1001

Chain	Residue
A	CYS58
A	PRO59
A	ASN63
A	CYS68
A	HIS71

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 1002

Chain	Residue
A	CYS146
A	CYS98
A	CYS101
A	GLN144
A	VAL145

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 1003

Chain	Residue
A	ASP456
A	ASP458
A	ASP460

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 2001

Chain	Residue
B	CYS1061
B	CYS1064
B	CYS1079
B	ILE1081

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S D 1001

Chain	Residue
D	CYS183
D	GLU185
D	CYS203
D	THR204
D	LEU205
D	CYS206
D	GLU207
D	GLU208
D	CYS209

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN N 1001

Chain	Residue
N	CYS7
N	CYS10
N	CYS44
N	CYS45

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN P 1001

Chain	Residue
P	CYS9
P	THR12
P	CYS26
P	CYS29

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN I 1001

Chain	Residue
I	CYS58
I	CYS61
I	ASN63
I	CYS68
I	HIS71
J	TYR1070

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN I 1002

Chain	Residue
I	CYS98
I	CYS101
I	GLN144
I	VAL145
I	CYS146

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG I 1003

Chain	Residue
I	ASP456
I	ASP458
I	ASP460

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN J 2001

Chain	Residue
J	CYS1061
J	CYS1064
J	CYS1079

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE F3S O 1001

Chain	Residue
O	CYS183
O	GLU185
O	CYS203
O	THR204
O	LEU205
O	CYS206
O	GLU207
O	GLU208
O	CYS209
O	ILE219

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN W 1001

Chain	Residue
W	CYS7
W	THR9
W	CYS10
W	CYS44
W	CYS45

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN X 1001

Chain	Residue
X	CYS9
X	THR12
X	CYS26
X	CYS29

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
D	ASN26-PRO66

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

Chain	Residue	Details
H	HIS14-GLU27

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

Chain	Residue	Details
K	THR28-GLN42

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

Chain	Residue	Details
N	LEU2-GLY11

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

Chain	Residue	Details
L	ILE17-PRO48

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

Chain	Residue	Details
B	GLY875-VAL887

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:18235446, ECO:0007744\|PDB:2PMZ, ECO:0007744\|PDB:3HKZ

Chain	Residue	Details
B	CYS1061
I	HIS71
I	CYS98
I	ASP456
I	ASP458
I	ASP460
B	CYS1064
B	CYS1079
J	CYS1061
J	CYS1064
J	CYS1079
W	CYS44
W	CYS45
I	CYS68

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:B8YB55

Chain	Residue	Details
B	HIS1082
J	HIS1082
O	CYS203
O	CYS209

site_id	SWS_FT_FI3
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00320, ECO:0000269\|PubMed:18235446, ECO:0007744\|PDB:2PA8, ECO:0007744\|PDB:3HKZ

Chain	Residue	Details
D	CYS206
O	CYS206

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00863, ECO:0007744\|PDB:3HKZ

Chain	Residue	Details
A	CYS146
I	CYS146

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P11512

Chain	Residue	Details
A	ARG573
A	CYS575
A	CYS580
A	HIS582
I	ARG573
I	CYS575
I	CYS580
I	HIS582

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)