4Q45: DNA Polymerase- damaged DNA complex

DNA Polymerase- damaged DNA complex. Determined by X-ray diffraction at 2.18 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.18 Å
Organisms: Escherichia coli, synthetic construct
Chains: 6
Atoms: 7,230
Mol. weight: 99.8 kDa
Ligands: MG, 1FZ
Released: 6 May 2015

Explore 4Q45 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q45 contains 38 α-helices and 36 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	8
β-strand	40	1	9
β-strand	41-44	4	8
α-helix	46-49	4
β-strand	58	1	9
α-helix	59-65	7
β-strand	70-72	3	8
α-helix	76-91	16
β-strand	97-99	3	7
β-strand	104-108	5	7
α-helix	119-134	16
β-strand	138-143	6	7
α-helix	146-155	10
β-strand	161-163	3	7
α-helix	169-174	6
β-strand	177	1	10
α-helix	178-180	3
α-helix	186-195	10
β-strand	199	1	10
α-helix	200-204	5
α-helix	208-226	19
α-helix	232-234	3
β-strand	242-253	12	11
α-helix	256-275	20
β-strand	282	1	12
β-strand	285-292	8	11
β-strand	297-303	7	11
β-strand	306	1	12
α-helix	309-323	15
β-strand	329-337	9	11
α-helix	338-339	2

Chain F: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	2
α-helix	35-37	3
β-strand	40	1	3
β-strand	41-44	4	2
α-helix	46-49	4
β-strand	58	1	3
α-helix	59-65	7
α-helix	69	1
β-strand	70-72	3	2
α-helix	76-91	16
β-strand	97-101	5	1
β-strand	104-108	5	1
α-helix	114-117	4
α-helix	119-127	9
α-helix	131-134	4
β-strand	138-143	6	1
α-helix	146-155	10
β-strand	161-163	3	1
α-helix	166-168	3
α-helix	169-175	7
β-strand	177	1	4
α-helix	178-180	3
α-helix	186-194	9
β-strand	199	1	4
α-helix	200-204	5
α-helix	208-215	8
α-helix	217-226	10
α-helix	232-234	3
β-strand	242-253	12	5
α-helix	256-277	22
β-strand	282	1	6
β-strand	285-292	8	5
β-strand	297-303	7	5
β-strand	306	1	6
α-helix	309-323	15
β-strand	329-337	9	5
α-helix	338-339	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase IV	A, F	protein	342	Escherichia coli	Q47155 (AlphaFold model)
DNA (5'-d(tpcptpapgpgp(rdg)ptpcpcptpapgpgpapcpcpc)-3')	B, G	DNA	18	synthetic construct
DNA (5'-d(tpcptpagpgpgptpcpcptpapgpgpapcpcpc)-3')	C, H	DNA	18	synthetic construct

Sequence of entity 1 (A, F), FASTA

>4Q45_1 DNA polymerase IV (chains A, F)
GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPT
GMALALCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSA
TLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLA
KIPGVGKVSAAKLEAMGLRTCGDVQACDLVMLLKRFGKFGRILWERSQGIDERDVNSERL
RKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP

Sequence of entity 2 (B, G), FASTA

>4Q45_2 DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG)P*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') (chains B, G)
TCTAGGXTCCTAGGACCC

Sequence of entity 3 (C, H), FASTA

>4Q45_3 DNA (5'-D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') (chains C, H)
TCTAGGGTCCTAGGACCC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
1FZ	5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidi…	C10 H18 N3 O13 P3	2

Primary citation

Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic. Kottur, J., Sharma, A., Gore, K.R. et al. Structure (2015) 23:56-67. DOI 10.1016/j.str.2014.10.019 · PubMed

Other PDB entries of the same protein (UniProt Q47155 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
5YUY 1.74 Å, DNA polymerase IV - DNA ternary complex 9
5YUZ 1.83 Å, DNA polymerase IV - DNA ternary complex 11
5YUU 1.89 Å, DNA polymerase IV - DNA ternary complex 4
1UNN 1.9 Å, Complex of beta-clamp processivity factor and little finger domain of PolIV
5YV2 1.9 Å, DNA polymerase IV - DNA ternary complex 14
5YUS 1.94 Å, DNA polymerase IV - DNA ternary complex 2
6IG1 1.97 Å, DNA polymerase IV - DNA ternary complex 10
5YV3 2.03 Å, DNA polymerase IV - DNA ternary complex 7
5YUR 2.04 Å, DNA polymerase IV - DNA ternary complex 1
5YUX 2.04 Å, DNA polymerase IV - DNA ternary complex 8
5YYD 2.05 Å, DNA polymerase IV - ternary complex 15

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