4JRP: E. coli Exonuclease I

Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide. Determined by X-ray diffraction at 1.95 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Escherichia coli
Chains: 4
Atoms: 8,474
Mol. weight: 120.04 kDa
Ligands: IPA, MG
Released: 8 May 2013

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

Secondary structure: helices and β-sheets

4JRP contains 69 α-helices and 29 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: 31 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	28-37	10	1
β-strand	42	1	1
β-strand	47-50	4	1
β-strand	51	1	2
α-helix	52-54	3
α-helix	61-67	7
α-helix	71-77	7
β-strand	79	1	2
α-helix	81-92	12
β-strand	97-100	4	1
α-helix	108-118	11
α-helix	125-127	3
α-helix	129-131	3
β-strand	133-134	2	1
α-helix	137-147	11
α-helix	153-155	3
β-strand	156	1	3
β-strand	162	1	3
α-helix	166-171	6
α-helix	183-200	18
α-helix	202-210	9
α-helix	214-218	5
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	276-283	8
α-helix	294-296	3
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	342-350	9
α-helix	363-365	3
α-helix	367-369	3
α-helix	374-385	12
α-helix	388-393	6
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

Chain B: 38 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	5
β-strand	28-37	10	5
β-strand	42-50	9	5
β-strand	51	1	6
α-helix	52-54	3
α-helix	61-67	7
α-helix	71-77	7
β-strand	79	1	6
α-helix	81-92	12
β-strand	97-100	4	5
α-helix	104-106	3
α-helix	108-118	11
α-helix	125-127	3
α-helix	129-131	3
β-strand	133-134	2	5
α-helix	137-147	11
β-strand	156	1	7
α-helix	161	1
β-strand	162	1	7
α-helix	163	1
α-helix	166-172	7
α-helix	183-200	18
α-helix	202-210	9
α-helix	214-218	5
β-strand	229-232	4	8
α-helix	234-236	3
α-helix	238-240	3
β-strand	243-251	9	8
β-strand	258-263	6	8
α-helix	269-273	5
α-helix	276-283	8
α-helix	294-296	3
β-strand	298-302	5	8
α-helix	303-305	3
β-strand	308-311	4	8
α-helix	312-314	3
α-helix	317-323	7
α-helix	327-339	13
α-helix	341-351	11
α-helix	354-355	2
α-helix	357-360	4
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	391-394	4
α-helix	402-414	13
α-helix	416-418	3
α-helix	421-434	14
α-helix	437-453	17
α-helix	458-473	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5cy-dT13	C, D	DNA	14
Exodeoxyribonuclease I	A, B	protein	478	Escherichia coli	P04995 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>4JRP_1 5cy-dT13 (chains C, D)
XTTTTTTTTTTTTT

Sequence of entity 2 (A, B), FASTA

>4JRP_2 Exodeoxyribonuclease I (chains A, B)
GSHMMNDGKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDY
LPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFY
RNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEH
SNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFG
AWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVP
VKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPF
TPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPG
TLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion. Korada, S.K., Johns, T.D., Smith, C.E. et al. Nucleic Acids Res (2013) 41:5887-5897. DOI 10.1093/nar/gkt278 · 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
3HL8 1.55 Å, Crystal structure of exonuclease I in complex with inhibitor BCBP
3HP9 1.6 Å, Crystal structure of SSB/Exonuclease I in complex with inhibitor CFAM
3C95 1.7 Å, Exonuclease I (apo)
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

Browse structure collections

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