3SM4: K131A Mutant of Lambda Exonuclease

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium. Determined by X-ray diffraction at 1.88 Å resolution. Released 20 Jul 2011.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Enterobacteria phage lambda
Chains: 5
Atoms: 6,607
Mol. weight: 86.77 kDa
Ligands: MG, PO4
Released: 20 Jul 2011

Explore 3SM4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SM4 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	22-27	6
β-strand	32-33	2	1
α-helix	34-36	3
α-helix	38-41	4
α-helix	49-51	3
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	146-149	4
α-helix	151-165	15
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	34-39	6
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	191	1
α-helix	193-216	24
α-helix	223-225	3

Chain C: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	14-16	3
α-helix	22-27	6
β-strand	32-33	2	5
α-helix	34-39	6
α-helix	50-51	2
α-helix	52-67	16
α-helix	75-83	9
α-helix	85-96	12
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	136-165	30
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(tpcpgpgptpapcpapgptpapg)-3'	D	DNA	12
5'-d(papgpcptpapcptpgptpapcpcpgpa)-3'	E	DNA	14

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

>3SM4_1 Exonuclease (chains A, B, C)
GSHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSY
FHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACS
PDGLCSDGNGLELACPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDP
RMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

Sequence of entity 2 (D), FASTA

>3SM4_2 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3' (chains D)
TCGGTACAGTAG

Sequence of entity 3 (E), FASTA

>3SM4_3 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
MG	Magnesium ion	Mg	2
PO4	Phosphate ion	O4 P	2

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:

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
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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