4WUZ: Lambda exonuclease

Crystal structure of lambda exonuclease in complex with DNA and Ca2+. Determined by X-ray diffraction at 2.38 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 2.38 Å
Organisms: Enterobacteria phage lambda, synthetic
Chains: 5
Atoms: 6,148
Mol. weight: 87.55 kDa
Ligands: PO4, CA
Released: 19 Nov 2014

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

Secondary structure: helices and β-sheets

4WUZ contains 34 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	14-16	3
α-helix	22-26	5
β-strand	32-33	2	1
α-helix	37-41	5
α-helix	50-51	2
α-helix	52-67	16
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	136-145	10
α-helix	146-148	3
α-helix	152-165	14
β-strand	169-175	7	2
β-strand	184-190	7	2
α-helix	193-217	25
α-helix	223-225	3

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	22-28	7
β-strand	32-33	2	3
α-helix	34-36	3
α-helix	38-41	4
α-helix	49-51	3
α-helix	52-67	16
α-helix	76-96	21
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	193-217	25

Chain C: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	14-16	3
α-helix	22-28	7
β-strand	32-33	2	5
α-helix	34-39	6
α-helix	50-51	2
α-helix	52-67	16
α-helix	75-96	22
β-strand	100-101	2	6
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	136-145	10
α-helix	146-149	4
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
DNA (5'-d(tpttpcpgpgptpapcpapgptpapg)-3')	D	DNA	14	synthetic
DNA (5'-d(papgpcptpapcptpgptpapcpcpgpa)-3')	E	DNA	14	synthetic

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

>4WUZ_1 Exonuclease (chains A, B, C)
GSHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSY
FHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACS
PDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDP
RMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

Sequence of entity 2 (D), FASTA

>4WUZ_2 DNA (5'-D(*TP*T*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3') (chains D)
TTTCGGTACAGTAG

Sequence of entity 3 (E), FASTA

>4WUZ_3 DNA (5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3') (chains E)
AGCTACTGTACCGA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
CA	Calcium ion	Ca	3

Primary citation

Crystal Structure of lambda Exonuclease in Complex with DNA and Ca(2+). Zhang, J., Pan, X., Bell, C.E. Biochemistry (2014) 53:7415-7425. DOI 10.1021/bi501155q · 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…
3SLP 2.3 Å, Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex
6M9K 2.3 Å, Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain
1AVQ 2.4 Å, Toroidal structure of lambda exonuclease determined at 2.4 Å

Browse structure collections

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