6M9K: Lambda exonuclease

Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain. Determined by X-ray diffraction at 2.3 Å resolution. Released 2 Jan 2019.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Escherichia phage lambda
Chains: 6
Atoms: 7,573
Mol. weight: 101.93 kDa
Released: 2 Jan 2019

Explore 6M9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M9K contains 57 α-helices and 31 β-strands across 6 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	37-41	5
α-helix	42-44	3
α-helix	49-51	3
α-helix	52-67	16
α-helix	71-72	2
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	136-143	8
α-helix	152-165	14
β-strand	169-175	7	2
β-strand	184-190	7	2
α-helix	193-216	24
α-helix	223-225	3

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	14-16	3
α-helix	22-28	7
β-strand	32	1	3
α-helix	37-40	4
α-helix	49-51	3
α-helix	52-67	16
α-helix	71-72	2
α-helix	75-96	22
β-strand	100-101	2	4
β-strand	106-107	2	5
β-strand	114	1	3
β-strand	115-116	2	5
β-strand	120-122	3	4
β-strand	127-131	5	4
α-helix	136-143	8
α-helix	152-165	14
β-strand	169-175	7	4
β-strand	184-190	7	4
α-helix	193-216	24

Chain C: 14 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	6
α-helix	34-36	3
α-helix	37-40	4
α-helix	50-51	2
α-helix	52-67	16
α-helix	75-96	22
β-strand	100-101	2	7
β-strand	106-107	2	6
β-strand	114-116	3	6
β-strand	120-122	3	7
β-strand	127-131	5	7
α-helix	136-145	10
α-helix	146-149	4
α-helix	152-165	14
β-strand	169-175	7	7
β-strand	184-190	7	7
α-helix	191	1
α-helix	193-216	24
α-helix	223-225	3

Chain D: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	195	1
β-strand	196	1	8
α-helix	197-198	2
α-helix	199-212	14
α-helix	216-220	5
α-helix	221-227	7
α-helix	235-237	3
β-strand	239	1	8
α-helix	240-257	18

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	196	1	9
α-helix	197-198	2
α-helix	199-211	13
α-helix	216-220	5
α-helix	221-228	8
α-helix	235-237	3
β-strand	239	1	9
α-helix	240-257	18

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	196	1	10
α-helix	197-198	2
α-helix	199-212	14
α-helix	216-220	5
α-helix	221-228	8
α-helix	235-237	3
β-strand	239	1	10
α-helix	240-255	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exonuclease	A, B, C	protein	226	Escherichia phage lambda	P03697
Recombination protein bet	D, E, F	protein	67	Escherichia phage lambda	P03698

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

>6M9K_1 Exonuclease (chains A, B, C)
MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHT
LLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDG
LCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMK
REGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

Sequence of entity 2 (D, E, F), FASTA

>6M9K_2 Recombination protein bet (chains D, E, F)
ITPVNDETMQEINTLLIALDKTWDDDLLPLCSQIFRRDIRASSELTQAEAVKALGFLKQK
AAEQKVA

Primary citation

Crystal structure of the Red beta C-terminal domain in complex with lambda Exonuclease reveals an unexpected homology with lambda Orf and an interaction with Escherichia coli single stranded DNA binding protein. Caldwell, B.J., Zakharova, E., Filsinger, G.T. et al. Nucleic Acids Res (2019) 47:1950-1963. DOI 10.1093/nar/gky1309 · 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
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

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