3HL8: Exonuclease I

Crystal structure of exonuclease I in complex with inhibitor BCBP. Determined by X-ray diffraction at 1.55 Å resolution. Released 19 Jan 2010.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Escherichia coli
Chains: 1
Atoms: 4,294
Mol. weight: 56.19 kDa
Ligands: BBP, MG
Released: 19 Jan 2010

Explore 3HL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HL8 contains 35 α-helices and 14 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: 35 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-18	9	1
α-helix	27	1
β-strand	28-36	9	1
β-strand	42-50	9	1
β-strand	51	1	2
α-helix	52-54	3
α-helix	61-67	7
α-helix	71-77	7
α-helix	78	1
β-strand	79	1	2
α-helix	80	1
α-helix	81-92	12
β-strand	97-101	5	1
α-helix	104-108	5
α-helix	109-118	10
α-helix	125-127	3
α-helix	129-131	3
β-strand	133-136	4	1
α-helix	137-147	11
β-strand	156	1	3
β-strand	162	1	3
α-helix	166-172	7
α-helix	185-200	16
α-helix	202-210	9
α-helix	214-219	6
β-strand	229-232	4	4
α-helix	234-236	3
α-helix	238-240	3
β-strand	243-251	9	4
β-strand	258-263	6	4
α-helix	269-273	5
α-helix	276-285	10
β-strand	298-302	5	4
β-strand	308-311	4	4
α-helix	312-314	3
α-helix	317-323	7
α-helix	327-338	12
α-helix	342-352	11
α-helix	363-365	3
α-helix	367-369	3
α-helix	371-373	3
α-helix	374-385	12
α-helix	388-390	3
α-helix	402-414	13
α-helix	416-418	3
α-helix	421-434	14
α-helix	437-453	17
α-helix	458-474	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exodeoxyribonuclease I	A	protein	482	Escherichia coli	P04995 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3HL8_1 Exodeoxyribonuclease I (chains A)
MMNDGKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQ
PGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNF
YDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNA
HDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWR
GNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKL
VHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPS
DNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLD
YAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVEHHHH
HH

Ligands and cofactors

ID	Name	Formula	Copies
BBP	(5R)-3-tert-butyl-1-(6-chloro-1,3-benzothiazol-2-yl)-4,5-dihydro-1H-pyrazol-5-ol	C14 H14 Cl N3 O S	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (EDO, DMS) are not listed.

Primary citation

Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance. Lu, D., Bernstein, D.A., Satyshur, K.A. et al. Proc Natl Acad Sci U S A (2010) 107:633-638. DOI 10.1073/pnas.0909191107 · PubMed

Other PDB entries of the same protein (UniProt P04995 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QXF 1.5 Å, Product bound structure of exonuclease I at 1.5 angstrom resolution
3HP9 1.6 Å, Crystal structure of SSB/Exonuclease I in complex with inhibitor CFAM
3C95 1.7 Å, Exonuclease I (apo)
4JRP 1.95 Å, Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide
4HCB 2.0 Å, The metal-free form of crystal structure of E.coli ExoI-ssDNA complex
1FXX 2.4 Å, The structure of exonuclease I suggests how processivity is achieved
3C94 2.7 Å, ExoI/SSB-Ct complex
4HCC 2.96 Å, The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex
4JRQ 3.0 Å, Crystal structure of E. coli Exonuclease I in complex with a 5cy-dA13 oligonucleotide
4JS4 3.1 Å, Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide
4JS5 3.5 Å, Crystal structure of E. coli Exonuclease I in complex with a dT13 oligonucleotide

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