5IIJ: DNA polymerase lambda

Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dCTP. Determined by X-ray diffraction at 1.72 Å resolution. Released 17 Aug 2016.

Method: X-ray diffraction
Resolution: 1.72 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,254
Mol. weight: 44.25 kDa
Ligands: DCT, MG
Released: 17 Aug 2016

Explore 5IIJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IIJ contains 21 α-helices and 10 β-strands across 1 chain. 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: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	256-269	14
α-helix	273-288	16
α-helix	292-293	2
α-helix	298-301	4
α-helix	307-319	13
α-helix	323-327	5
α-helix	332-339	8
α-helix	346-354	9
α-helix	360-366	7
α-helix	371-378	8
α-helix	380-384	5
β-strand	387-388	2	1
α-helix	389-404	16
β-strand	411-414	4	2
α-helix	416-419	4
β-strand	424-425	2	1
β-strand	428-433	6	2
α-helix	444-453	10
β-strand	457-462	6	2
β-strand	472-477	6	2
α-helix	484-486	3
β-strand	487-493	7	2
α-helix	496-498	3
α-helix	499-507	9
α-helix	510-522	13
β-strand	525-527	3	3
β-strand	532-534	3	3
β-strand	550	1	3
α-helix	551-552	2
α-helix	556-562	7
α-helix	570-573	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase lambda	A	protein	334	Homo sapiens	Q9UGP5 (AlphaFold model)
DNA (5'-d(pgpcpcpg)-3')	D	DNA	4	synthetic construct
DNA (5'-d(cpapgptpap(doc))-3')	P	DNA	6	synthetic construct
DNA (5'-D(CPGPGPCP(8OG)PGPTPAPCPTP*G)-3')	T	DNA	11	synthetic construct

Sequence of entity 1 (A), FASTA

>5IIJ_1 DNA polymerase lambda (chains A)
AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACS
IPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLE
DIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRG
KATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPG
PGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTH
GCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Sequence of entity 2 (D), FASTA

>5IIJ_2 DNA (5'-D(P*GP*CP*CP*G)-3') (chains D)
GCCG

Sequence of entity 3 (P), FASTA

>5IIJ_3 DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3') (chains P)
CAGTAC

Sequence of entity 4 (T), FASTA

>5IIJ_4 DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3') (chains T)
CGGCGGTACTG

Ligands and cofactors

ID	Name	Formula	Copies
DCT	2',3'-dideoxycytidine 5'-triphosphate	C9 H16 N3 O12 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (NA) are not listed.

Primary citation

A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. Burak, M.J., Guja, K.E., Hambardjieva, E. et al. EMBO J (2016) 35:2045-2059. DOI 10.15252/embj.201694332 · PubMed

Other PDB entries of the same protein (UniProt Q9UGP5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M07 1.57 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M49 1.6 Å, DNA Polymerase Lambda, TTP:At Mn2+ Reaction State Ternary Complex, 5 min
9NPU 1.63 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M47 1.65 Å, DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min
2BCQ 1.65 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp
7M09 1.65 Å, Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate…
7M4B 1.66 Å, DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min
7M08 1.7 Å, Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M4L 1.7 Å, DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min
7M4K 1.72 Å, DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex
2BCR 1.75 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp
5III 1.8 Å, Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a…

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