3SLP: Lambda Exonuclease

Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Jul 2011.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Enterobacteria phage lambda
Chains: 5
Atoms: 6,460
Mol. weight: 86.47 kDa
Ligands: PO4, CA
Released: 20 Jul 2011

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

Secondary structure: helices and β-sheets

3SLP contains 36 α-helices and 24 β-strands across 3 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: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	14-16	3
α-helix	22-28	7
β-strand	32-33	2	1
α-helix	34-36	3
α-helix	37-41	5
α-helix	49-51	3
α-helix	52-67	16
α-helix	70-73	4
α-helix	75-96	22
β-strand	100-101	2	2
β-strand	106-107	2	1
β-strand	114-116	3	1
β-strand	120-122	3	2
β-strand	127-131	5	2
α-helix	136-149	14
α-helix	153-165	13
β-strand	169-175	7	2
β-strand	184-190	7	2
α-helix	193-216	24
α-helix	223-225	3

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	22-27	6
β-strand	32-33	2	3
α-helix	34-36	3
α-helix	37-40	4
α-helix	52-67	16
α-helix	76-83	8
α-helix	85-96	12
β-strand	100-101	2	4
β-strand	106-107	2	3
β-strand	114-116	3	3
β-strand	120-122	3	4
β-strand	127-131	5	4
α-helix	136-145	10
α-helix	146-149	4
α-helix	152-165	14
β-strand	169-175	7	4
β-strand	184-190	7	4
α-helix	193-216	24
α-helix	223-225	3

Chain C: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	22-28	7
β-strand	32-33	2	5
α-helix	37-40	4
α-helix	52-67	16
α-helix	71-73	3
α-helix	76-83	8
α-helix	85-96	12
β-strand	100-101	2	6
α-helix	102-103	2
β-strand	106-107	2	5
β-strand	114-116	3	5
β-strand	120-122	3	6
β-strand	127-131	5	6
α-helix	136-149	14
α-helix	152-165	14
β-strand	169-175	7	6
β-strand	184-190	7	6
α-helix	193-216	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exonuclease	A, B, C	protein	229	Enterobacteria phage lambda	P03697
5'-d(gpcpgpapcptpapgptpcpgpc)-3'	D, E	DNA	12

Sequence of entity 1 (A, B, C), FASTA

>3SLP_1 Exonuclease (chains A, B, C)
GSHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSY
FHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACS
PDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDP
RMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

Sequence of entity 2 (D, E), FASTA

>3SLP_2 5'-D(*GP*CP*GP*AP*CP*TP*AP*GP*TP*CP*GP*C)-3' (chains D, E)
GCGACTAGTCGC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
CA	Calcium ion	Ca	3

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

Primary citation

Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity. Zhang, J., McCabe, K.A., Bell, C.E. Proc Natl Acad Sci U S A (2011) 108:11872-11877. DOI 10.1073/pnas.1103467108 · PubMed

Other PDB entries of the same protein (UniProt P03697), best resolution first:

3SM4 1.88 Å, Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a…
6M9K 2.3 Å, Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain
4WUZ 2.38 Å, Crystal structure of lambda exonuclease in complex with DNA and Ca2+
1AVQ 2.4 Å, Toroidal structure of lambda exonuclease determined at 2.4 Å

Browse structure collections

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