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(-) Description

Title :  CRYSTAL STRUCTURE OF THE K131A MUTANT OF LAMBDA EXONUCLEASE IN COMPLEX WITH A 5'-PHOSPHORYLATED 14-MER/12-MER DUPLEX AND MAGNESIUM
 
Authors :  C. E. Bell, J. Zhang
Date :  27 Jun 11  (Deposition) - 20 Jul 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Homologous Recombination, Dna Repair, Recombineering, Single-Strand Annealing, Type Ii Restriction Endonuclease Fold, 5'-3' Dsdna Exonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, K. A. Mccabe, C. E. Bell
Crystal Structures Of {Lambda} Exonuclease In Complex With Dna Suggest An Electrostatic Ratchet Mechanism For Processivity.
Proc. Natl. Acad. Sci. Usa V. 108 11872 2011
PubMed-ID: 21730170  |  Reference-DOI: 10.1073/PNAS.1103467108

(-) Compounds

Molecule 1 - EXONUCLEASE
    Chains: A, B, C
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-AI
    Expression System Taxid: 562
    Expression System Vector Type: PET-14B
    Gene: EXO, LAMBDA EXONUCLEASE, RED-ALPHA, REDX
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
 
Molecule 2 - 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'
    Chains: E
    Engineered: YES
    Other Details: 5'-PHOSPHORYLATED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:17 , TRP A:24 , LEU A:27 , ARG A:28 , PRO A:104 , ILE A:105BINDING SITE FOR RESIDUE PO4 A 227
2AC2SOFTWAREALA A:34 , SER A:35 , SER A:117 , CL A:229 , HOH A:299BINDING SITE FOR RESIDUE CL A 228
3AC3SOFTWARETHR A:33 , CYS A:116 , SER A:117 , CL A:228 , HOH A:394BINDING SITE FOR RESIDUE CL A 229
4AC4SOFTWAREASP B:119 , GLU B:129 , LEU B:130 , HOH B:550 , DG E:2 , HOH E:543BINDING SITE FOR RESIDUE MG B 227
5AC5SOFTWAREARG C:28 , THR C:33 , ALA C:34 , SER C:35 , ALA C:115 , CYS C:116 , SER C:117 , HOH C:527BINDING SITE FOR RESIDUE PO4 C 227
6AC6SOFTWAREASP B:119 , HOH B:277 , HOH B:305 , HOH B:310 , DA E:1 , DG E:2BINDING SITE FOR RESIDUE MG E 15

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SM4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:19 -Gly A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SM4)

(-) Exons   (0, 0)

(no "Exon" information available for 3SM4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:225
 aligned with EXO_LAMBD | P03697 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
            EXO_LAMBD     2 TPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3sm4a_ A: lambda exonuclease                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.........hhhhhhhh...ee...hhhhhh........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sm4 A   2 TPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELACPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with EXO_LAMBD | P03697 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:228
                              1                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
            EXO_LAMBD     - --MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3sm4b_ B: lambda exonuclease                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.........hhhhhhhh...ee.hhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sm4 B  -1 SHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELACPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        


Chain C from PDB  Type:PROTEIN  Length:229
 aligned with EXO_LAMBD | P03697 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:229
                               1                                                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
            EXO_LAMBD     - ---MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3sm4c_ C: lambda exonuclease                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhh...hhhhhhhh...ee.hhhhhh..........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sm4 C  -2 GSHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELACPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         


Chain D from PDB  Type:DNA  Length:12
                                            
                 3sm4 D   1 TCGGTACAGTAG  12
                                    10  


Chain E from PDB  Type:DNA  Length:14
                                              
                 3sm4 E   1 AGCTACTGTACCGA  14
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SM4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SM4)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (EXO_LAMBD | P03697)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  3sm4
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  EXO_LAMBD | P03697
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  3.1.11.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EXO_LAMBD | P03697: 1avq 3slp 4wuz

(-) Related Entries Specified in the PDB File

3slp CRYSTAL STRUCTURE OF LAMBDA EXONUCLEASE IN COMPLEX WITH A 12 BP SYMMETRIC DNA DUPLEX