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(-) Description

Title :  TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS
 
Authors :  R. A. Kovall, B. W. Matthews
Date :  18 Sep 97  (Deposition) - 18 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Deoxyribonuclease, Dna Recombination And Repair, 5'-3' Exonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kovall, B. W. Matthews
Toroidal Structure Of Lambda-Exonuclease.
Science V. 277 1824 1997
PubMed-ID: 9295273  |  Reference-DOI: 10.1126/SCIENCE.277.5333.1824
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMBDA EXONUCLEASE
    Cell Line: BL21
    Chains: A, B, C
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28(A+)
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
    Synonym: RED ALPHA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:28 , THR A:33 , ALA A:34 , SER A:35 , CYS A:116 , SER A:117 , GLN A:157 , HOH A:267BINDING SITE FOR RESIDUE PO4 A 227
2AC2SOFTWAREARG B:28 , THR B:33 , ALA B:34 , SER B:35 , CYS B:116 , SER B:117 , GLN B:157 , HOH B:309BINDING SITE FOR RESIDUE PO4 B 227
3AC3SOFTWAREARG C:28 , THR C:33 , ALA C:34 , SER C:35 , CYS C:116 , SER C:117 , HOH C:247BINDING SITE FOR RESIDUE PO4 C 227
4AC4SOFTWARESER A:198BINDING SITE FOR RESIDUE ACT A 228
5AC5SOFTWARESER B:198BINDING SITE FOR RESIDUE ACT B 228
6AC6SOFTWARELYS C:194 , TYR C:195 , SER C:198BINDING SITE FOR RESIDUE ACT C 228
7AC7SOFTWARETHR C:2 , ILE C:5 , ILE C:6 , ASP C:109 , GLU C:110 , HOH C:237 , HOH C:278BINDING SITE FOR RESIDUE ACT C 229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AVQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AVQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AVQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AVQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1AVQ)

(-) 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: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 d1avqa_ A: lambda exonuclease                                                                                                                                                                                                        SCOP domains
               CATH domains 1avqA00 A:-1-226  [code=3.90.320.10, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhh...hhh.....hhhhh.......hhhhhhh...........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee....ee......eee...eee....eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh......hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1avq A  -1 SHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        


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 d1avqb_ B: lambda exonuclease                                                                                                                                                                                                        SCOP domains
               CATH domains 1avqB00 B:-1-226  [code=3.90.320.10, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhh...hhh.....hhhhh.......hhhhhhh...........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee....ee......eee...eee....eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh......hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1avq B  -1 SHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 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: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 d1avqc_ C: lambda exonuclease                                                                                                                                                                                                     SCOP domains
               CATH domains 1avqC00 C:2-226  [code=3.90.320.10, no name defined]                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhh.....hhhhh.......hhhhhhh...........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee....ee......eee...eee....eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh......hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1avq C   2 TPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AVQ)

(-) 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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  1avq
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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: 3slp 3sm4 4wuz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AVQ)