Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4ESV

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003677	molecular_function	DNA binding
A	0003678	molecular_function	DNA helicase activity
A	0004386	molecular_function	helicase activity
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0006260	biological_process	DNA replication
A	0006269	biological_process	DNA replication, synthesis of primer
A	0016787	molecular_function	hydrolase activity
A	0016853	molecular_function	isomerase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0042802	molecular_function	identical protein binding
A	0043139	molecular_function	5'-3' DNA helicase activity
A	1990077	cellular_component	primosome complex
B	0000166	molecular_function	nucleotide binding
B	0003677	molecular_function	DNA binding
B	0003678	molecular_function	DNA helicase activity
B	0004386	molecular_function	helicase activity
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0006260	biological_process	DNA replication
B	0006269	biological_process	DNA replication, synthesis of primer
B	0016787	molecular_function	hydrolase activity
B	0016853	molecular_function	isomerase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0042802	molecular_function	identical protein binding
B	0043139	molecular_function	5'-3' DNA helicase activity
B	1990077	cellular_component	primosome complex
C	0000166	molecular_function	nucleotide binding
C	0003677	molecular_function	DNA binding
C	0003678	molecular_function	DNA helicase activity
C	0004386	molecular_function	helicase activity
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0006260	biological_process	DNA replication
C	0006269	biological_process	DNA replication, synthesis of primer
C	0016787	molecular_function	hydrolase activity
C	0016853	molecular_function	isomerase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0042802	molecular_function	identical protein binding
C	0043139	molecular_function	5'-3' DNA helicase activity
C	1990077	cellular_component	primosome complex
D	0000166	molecular_function	nucleotide binding
D	0003677	molecular_function	DNA binding
D	0003678	molecular_function	DNA helicase activity
D	0004386	molecular_function	helicase activity
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0006260	biological_process	DNA replication
D	0006269	biological_process	DNA replication, synthesis of primer
D	0016787	molecular_function	hydrolase activity
D	0016853	molecular_function	isomerase activity
D	0016887	molecular_function	ATP hydrolysis activity
D	0042802	molecular_function	identical protein binding
D	0043139	molecular_function	5'-3' DNA helicase activity
D	1990077	cellular_component	primosome complex
E	0000166	molecular_function	nucleotide binding
E	0003677	molecular_function	DNA binding
E	0003678	molecular_function	DNA helicase activity
E	0004386	molecular_function	helicase activity
E	0005524	molecular_function	ATP binding
E	0005829	cellular_component	cytosol
E	0006260	biological_process	DNA replication
E	0006269	biological_process	DNA replication, synthesis of primer
E	0016787	molecular_function	hydrolase activity
E	0016853	molecular_function	isomerase activity
E	0016887	molecular_function	ATP hydrolysis activity
E	0042802	molecular_function	identical protein binding
E	0043139	molecular_function	5'-3' DNA helicase activity
E	1990077	cellular_component	primosome complex
F	0000166	molecular_function	nucleotide binding
F	0003677	molecular_function	DNA binding
F	0003678	molecular_function	DNA helicase activity
F	0004386	molecular_function	helicase activity
F	0005524	molecular_function	ATP binding
F	0005829	cellular_component	cytosol
F	0006260	biological_process	DNA replication
F	0006269	biological_process	DNA replication, synthesis of primer
F	0016787	molecular_function	hydrolase activity
F	0016853	molecular_function	isomerase activity
F	0016887	molecular_function	ATP hydrolysis activity
F	0042802	molecular_function	identical protein binding
F	0043139	molecular_function	5'-3' DNA helicase activity
F	1990077	cellular_component	primosome complex
G	0000166	molecular_function	nucleotide binding
G	0003677	molecular_function	DNA binding
G	0003678	molecular_function	DNA helicase activity
G	0004386	molecular_function	helicase activity
G	0005524	molecular_function	ATP binding
G	0005829	cellular_component	cytosol
G	0006260	biological_process	DNA replication
G	0006269	biological_process	DNA replication, synthesis of primer
G	0016787	molecular_function	hydrolase activity
G	0016853	molecular_function	isomerase activity
G	0016887	molecular_function	ATP hydrolysis activity
G	0042802	molecular_function	identical protein binding
G	0043139	molecular_function	5'-3' DNA helicase activity
G	1990077	cellular_component	primosome complex
H	0000166	molecular_function	nucleotide binding
H	0003677	molecular_function	DNA binding
H	0003678	molecular_function	DNA helicase activity
H	0004386	molecular_function	helicase activity
H	0005524	molecular_function	ATP binding
H	0005829	cellular_component	cytosol
H	0006260	biological_process	DNA replication
H	0006269	biological_process	DNA replication, synthesis of primer
H	0016787	molecular_function	hydrolase activity
H	0016853	molecular_function	isomerase activity
H	0016887	molecular_function	ATP hydrolysis activity
H	0042802	molecular_function	identical protein binding
H	0043139	molecular_function	5'-3' DNA helicase activity
H	1990077	cellular_component	primosome complex
I	0000166	molecular_function	nucleotide binding
I	0003677	molecular_function	DNA binding
I	0003678	molecular_function	DNA helicase activity
I	0004386	molecular_function	helicase activity
I	0005524	molecular_function	ATP binding
I	0005829	cellular_component	cytosol
I	0006260	biological_process	DNA replication
I	0006269	biological_process	DNA replication, synthesis of primer
I	0016787	molecular_function	hydrolase activity
I	0016853	molecular_function	isomerase activity
I	0016887	molecular_function	ATP hydrolysis activity
I	0042802	molecular_function	identical protein binding
I	0043139	molecular_function	5'-3' DNA helicase activity
I	1990077	cellular_component	primosome complex
J	0000166	molecular_function	nucleotide binding
J	0003677	molecular_function	DNA binding
J	0003678	molecular_function	DNA helicase activity
J	0004386	molecular_function	helicase activity
J	0005524	molecular_function	ATP binding
J	0005829	cellular_component	cytosol
J	0006260	biological_process	DNA replication
J	0006269	biological_process	DNA replication, synthesis of primer
J	0016787	molecular_function	hydrolase activity
J	0016853	molecular_function	isomerase activity
J	0016887	molecular_function	ATP hydrolysis activity
J	0042802	molecular_function	identical protein binding
J	0043139	molecular_function	5'-3' DNA helicase activity
J	1990077	cellular_component	primosome complex
K	0000166	molecular_function	nucleotide binding
K	0003677	molecular_function	DNA binding
K	0003678	molecular_function	DNA helicase activity
K	0004386	molecular_function	helicase activity
K	0005524	molecular_function	ATP binding
K	0005829	cellular_component	cytosol
K	0006260	biological_process	DNA replication
K	0006269	biological_process	DNA replication, synthesis of primer
K	0016787	molecular_function	hydrolase activity
K	0016853	molecular_function	isomerase activity
K	0016887	molecular_function	ATP hydrolysis activity
K	0042802	molecular_function	identical protein binding
K	0043139	molecular_function	5'-3' DNA helicase activity
K	1990077	cellular_component	primosome complex
L	0000166	molecular_function	nucleotide binding
L	0003677	molecular_function	DNA binding
L	0003678	molecular_function	DNA helicase activity
L	0004386	molecular_function	helicase activity
L	0005524	molecular_function	ATP binding
L	0005829	cellular_component	cytosol
L	0006260	biological_process	DNA replication
L	0006269	biological_process	DNA replication, synthesis of primer
L	0016787	molecular_function	hydrolase activity
L	0016853	molecular_function	isomerase activity
L	0016887	molecular_function	ATP hydrolysis activity
L	0042802	molecular_function	identical protein binding
L	0043139	molecular_function	5'-3' DNA helicase activity
L	1990077	cellular_component	primosome complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MES W 101

Chain	Residue
H	SER364
I	ARG365
I	GLN369
W	DT12

site_id	AC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE GDP A 502

Chain	Residue
A	ALA218
A	ARG250
A	ALA260
A	GLN261
A	PHE431
A	LYS433
A	CA503
A	ALF504
A	CA506
F	GLN419
F	ASN421
F	GLY422
A	SER213
A	VAL214
A	GLY215
A	LYS216
A	THR217

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA A 503

Chain	Residue
A	THR217
A	GLU241
A	ASP320
A	GDP502
A	ALF504

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALF A 504

Chain	Residue
A	PRO212
A	SER213
A	LYS216
A	GLU241
A	GLN362
A	GDP502
A	CA503
F	LYS418
F	ARG420

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA A 505

Chain	Residue
A	SER378

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA A 506

Chain	Residue
A	SER213
A	GDP502
F	VAL424

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 507

Chain	Residue
A	GLU111
A	ASP391

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GDP C 501

Chain	Residue
B	GLN419
B	ASN421
B	GLY422
B	PRO423
C	SER213
C	VAL214
C	GLY215
C	LYS216
C	THR217
C	ALA218
C	ARG250
C	ALA260
C	LYS433
C	GLU434
C	CA502
C	ALF503

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA C 502

Chain	Residue
C	THR217
C	GLU241
C	ASP320
C	GDP501
C	ALF503

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALF C 503

Chain	Residue
B	LYS418
B	ARG420
C	PRO212
C	SER213
C	LYS216
C	GLU241
C	GLN362
C	GDP501
C	CA502

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ALF C 504

Chain	Residue
C	GLN388
C	LYS418
C	ARG420
D	LYS216
D	GLU241
D	GLN362
D	GDP501
D	CA502

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MES C 505

Chain	Residue
C	SER35
C	GLU36
C	ILE37
C	ILE39
C	ASP42
C	ARG117
C	LYS154
C	HIS155

site_id	BC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE GDP D 501

Chain	Residue
D	ARG264
D	ARG398
D	ASN436
D	CA502
D	HOH601
C	GLN419
C	ASN421
C	GLY422
C	ALF504
D	SER213
D	GLY215
D	LYS216
D	THR217
D	ALA218
D	ARG250
D	ALA260
D	GLN261

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA D 502

Chain	Residue
C	ALF504
D	THR217
D	GLU241
D	MET242
D	GDP501

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ALF D 503

Chain	Residue
D	LYS418
D	ARG420
E	PRO212
E	LYS216
E	GLU241
E	GLN362
E	GDP501
E	CA502

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA D 504

Chain	Residue
D	ASN285
G	GLU135

site_id	BC8
Number of Residues	20
Details	BINDING SITE FOR RESIDUE GDP E 501

Chain	Residue
D	GLN419
D	ASN421
D	GLY422
D	PRO423
D	ALF503
E	SER213
E	VAL214
E	GLY215
E	LYS216
E	THR217
E	ALA218
E	MET242
E	ARG250
E	ALA260
E	GLN261
E	ARG264
E	PHE431
E	LYS433
E	ASN436
E	CA502

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA E 502

Chain	Residue
D	ALF503
E	THR217
E	GLU241
E	MET242
E	ASP320
E	GDP501

site_id	CC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALF E 503

Chain	Residue
E	LYS418
E	ARG420
F	PRO212
F	SER213
F	LYS216
F	GLU241
F	GLN362
F	GDP501
F	CA502

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MES E 504

Chain	Residue
E	SER13
E	LYS112
E	ARG116
F	GLU133

site_id	CC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GDP F 501

Chain	Residue
E	GLN419
E	ASN421
E	GLY422
E	ALF503
F	SER213
F	VAL214
F	GLY215
F	LYS216
F	THR217
F	ALA218
F	MET242
F	ARG250
F	GLN261
F	ARG398
F	LYS433
F	CA502

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA F 502

Chain	Residue
E	ALF503
F	THR217
F	GLU241
F	MET242
F	ASP320
F	GDP501

site_id	CC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GDP G 501

Chain	Residue
G	SER213
G	VAL214
G	GLY215
G	LYS216
G	THR217
G	ALA218
G	ARG250
G	GLN261
G	LYS433
G	ASN436
G	ALF502
L	GLN419
L	GLY422
L	PRO423
L	VAL424

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ALF G 502

Chain	Residue
G	LYS216
G	THR217
G	GLU241
G	GLN362
G	GDP501
L	GLN388
L	LYS418
L	ARG420

site_id	CC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GDP I 501

Chain	Residue
H	GLN419
H	ASN421
H	GLY422
H	PRO423
H	VAL424
I	SER213
I	GLY215
I	LYS216
I	THR217
I	ALA218
I	ARG250
I	ALA260
I	GLN261
I	LYS433
I	CA502
I	ALF503

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA I 502

Chain	Residue
I	THR217
I	GLU241
I	MET242
I	GDP501
I	ALF503

site_id	CC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ALF I 503

Chain	Residue
H	GLN388
H	LYS418
H	ARG420
I	LYS216
I	GLU241
I	GLN362
I	GDP501
I	CA502

site_id	DC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MES I 504

Chain	Residue
I	GLY129
I	GLU133

site_id	DC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GDP J 501

Chain	Residue
I	GLN419
I	ASN421
I	GLY422
I	VAL424
J	SER213
J	GLY215
J	LYS216
J	THR217
J	ALA218
J	ARG250
J	ALA260
J	GLN261
J	LYS433
J	ALF502

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ALF J 502

Chain	Residue
I	LYS418
I	ARG420
J	LYS216
J	THR217
J	GLU241
J	MET242
J	GLN362
J	GDP501

site_id	DC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GDP K 501

Chain	Residue
J	GLN419
J	ASN421
J	GLY422
J	VAL424
K	SER213
K	GLY215
K	LYS216
K	THR217
K	ALA218
K	ARG250
K	ALA260
K	LYS433
K	GLU434
K	ASN436
K	ALF502

site_id	DC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALF K 502

Chain	Residue
J	GLN388
J	LYS418
J	ARG420
K	PRO212
K	SER213
K	LYS216
K	THR217
K	GLU241
K	GDP501

site_id	DC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GDP L 501

Chain	Residue
K	GLN419
K	GLY422
K	PRO423
K	VAL424
L	SER213
L	GLY215
L	LYS216
L	THR217
L	ALA218
L	ARG250
L	GLN261
L	LYS433
L	ALF502
L	CA503

site_id	DC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALF L 502

Chain	Residue
K	GLN388
K	LYS418
K	ARG420
L	PRO212
L	LYS216
L	GLU241
L	GLN362
L	GDP501
L	CA503

site_id	DC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA L 503

Chain	Residue
L	THR217
L	ASP320
L	GDP501
L	ALF502

Functional Information from PROSITE/UniProt

site_id	PS00039
Number of Residues	9
Details	DEAD_ATP_HELICASE DEAD-box subfamily ATP-dependent helicases signature. LLDEADRkI

Chain	Residue	Details
A	LEU139-ILE147

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"12235389","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23022319","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	108
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23022319","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4ESV","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23022319","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23022319","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4ESV","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Site: {"description":"Gamma-phosphate sensor","evidences":[{"source":"PubMed","id":"12235389","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	143
Details	Region: {"description":"Linker helix","evidences":[{"source":"PubMed","id":"17947583","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23022319","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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