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(-) Description

Title :  CRYSTAL STRUCTURE OF LAMBDA EXONUCLEASE IN COMPLEX WITH A 12 BP SYMMETRIC DNA DUPLEX
 
Authors :  C. E. Bell, J. Zhang
Date :  24 Jun 11  (Deposition) - 20 Jul 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  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 Taxid: 562
    Gene: EXO, RED-ALPHA, REDX
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
 
Molecule 2 - 5'-D(*GP*CP*GP*AP*CP*TP*AP*GP*TP*CP*GP*C)-3'
    Chains: D, E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:119 , GLU A:129 , HOH A:312 , HOH A:367 , HOH A:488BINDING SITE FOR RESIDUE CA A 227
2AC2SOFTWAREARG A:28 , THR A:33 , ALA A:34 , SER A:35 , CYS A:116 , SER A:117 , HOH A:271BINDING SITE FOR RESIDUE PO4 A 228
3AC3SOFTWAREASP B:119 , GLU B:129 , LEU B:130 , HOH B:231 , HOH B:232 , HOH B:307BINDING SITE FOR RESIDUE CA B 227
4AC4SOFTWAREARG B:28 , THR B:33 , ALA B:34 , SER B:35 , ALA B:115 , CYS B:116 , SER B:117 , GLN B:157 , HOH B:266 , HOH B:267BINDING SITE FOR RESIDUE PO4 B 229
5AC5SOFTWARESER C:117 , ASP C:119 , GLU C:129 , HOH C:336 , HOH C:460 , HOH C:481BINDING SITE FOR RESIDUE CA C 227
6AC6SOFTWAREARG C:108 , ARG C:166BINDING SITE FOR RESIDUE CL C 228
7AC7SOFTWAREARG C:28 , THR C:33 , ALA C:34 , SER C:35 , CYS C:116 , SER C:117 , HOH C:332 , HOH C:460BINDING SITE FOR RESIDUE PO4 C 229

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:96 -Gly A:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SLP)

(-) 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:226
 aligned with EXO_LAMBD | P03697 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            EXO_LAMBD     1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3slpa_ A: lambda exonuclease                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhh...hhhhhhhhh..ee..hhhhhhh........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee....eeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3slp A   1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


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

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            EXO_LAMBD     1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3slpb_ 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....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3slp B   1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


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

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            EXO_LAMBD     1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
               SCOP domains d3slpc_ C: lambda exonuclease                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.........hhhhhhhhh..ee..hhhhhh.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3slp C   1 MTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain D from PDB  Type:DNA  Length:12
                                            
                 3slp D   1 GCGACTAGTCGC  12
                                    10  


Chain E from PDB  Type:DNA  Length:12
                                            
                 3slp E   1 GCGACTAGTCGC  12
                                    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 3SLP)

(-) Pfam Domains  (0, 0)

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

(-) 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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  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 3sm4 4wuz

(-) Related Entries Specified in the PDB File

3sm4 CRYSTAL STRUCTURE OF THE K131A MUTANT OF LAMBDA EXONUCLEASE IN COMPLEX WITH A 5'-PHOSPHORYLATED 14-MER/12-MER DUPLEX AND MAGNESIUM