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(-) Description

Title :  T5 5'-EXONUCLEASE MUTANT K83A
 
Authors :  T. A. Ceska, D. Suck, J. R. Sayers
Date :  19 Nov 98  (Deposition) - 02 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Exonuclease, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Garforth, T. A. Ceska, D. Suck, J. R. Sayers
Mutagenesis Of Conserved Lysine Residues In Bacteriophage T5 5'-3' Exonuclease Suggests Separate Mechanisms Of Endo-And Exonucleolytic Cleavage.
Proc. Natl. Acad. Sci. Usa V. 96 38 1999
PubMed-ID: 9874768  |  Reference-DOI: 10.1073/PNAS.96.1.38
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-EXONUCLEASE
    Chains: A, B
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: D15
    Expression System Strain: M72
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: D15
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T5
    Organism Taxid: 10726
    Strain: M72
    Synonym: 5'-NUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XO1)

(-) Sites  (0, 0)

(no "Site" information available for 1XO1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XO1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:234 -Pro A:235
2Leu B:234 -Pro B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XO1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XO1)

(-) Exons   (0, 0)

(no "Exon" information available for 1XO1)

(-) Sequences/Alignments

Asymmetric 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:245
 aligned with EXO5_BPT5 | P06229 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:272
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  
            EXO5_BPT5    19 RRNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
               SCOP domains d1xo1a2 A:19-185        T5 5'-exonuclease                                                                                                                              d1xo1a1 A:186-290 T5 5'-exonuclease                                                                       SCOP domains
               CATH domains -1xo1A02 A:20-17       9,A:261-286 5'-nuclease                                                                                                                   -1xo1A01 A:181-260 5' to 3' exonuclease, C-terminal subdomain                    1xo1A02 A:20-179,A:261-286---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.-------..hhhhhhhhhhhhhh..eeeeeeee.....hhhh.......--------------------.hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eeee...hhhhhh....eeee.........hhhhhhhh....hhhhhhhhhhh..hhh.........hhhhhhhhhhh..hhhhhhh.......hhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xo1 A  19 RRNLMIVDGTNLGFRF-------PFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYA--------------------FFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
                                    28     |   -   |    48        58        68        78    |    -         -     | 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  
                                          34      42                                       83                  104                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with EXO5_BPT5 | P06229 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:272
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  
            EXO5_BPT5    19 RRNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
               SCOP domains d1xo1b2 B:19-185        T5 5'-exonuclease                                                                                                                              d1xo1b1 B:186-290 T5 5'-exonuclease                                                                       SCOP domains
               CATH domains -1xo1B02 B:20-17       9,B:261-286 5'-nuclease                                                                                                                   -1xo1B01 B:181-260 5' to 3' exonuclease, C-terminal subdomain                    1xo1B02 B:20-179,B:261-286---- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------5_3_exonuc-1xo1B01 B:188-274                                                           ---------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------5_3_exonuc-1xo1B02 B:188-274                                                           ---------------- Pfam domains (2)
           Pfam domains (3) -5_3_exonuc_N-1x       o1B03 B:20-188                                                                                                                                     ------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -5_3_exonuc_N-1x       o1B04 B:20-188                                                                                                                                     ------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author ..eeeeeehhhhhhh.-------..hhhhhhhhhhhhhh..eeeeeee......hhhhhh.....--------------------.hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhh...eeee...hhhhh.....eeee.........hhhhhhhh....hhhhhhhhhhh..hhh.........hhhhhhhhhhh..hhhhhhh.......hhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xo1 B  19 RRNLMIVDGTNLGFRF-------PFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYA--------------------FFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
                                    28     |   -   |    48        58        68        78    |    -         -     | 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  
                                          34      42                                       83                  104
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: 5_3_exonuc_C (16)
(-)
Clan: PIN (27)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EXO5_BPT5 | P06229)
molecular function
    GO:0008409    5'-3' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
    GO:0017108    5'-flap endonuclease activity    Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.

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        EXO5_BPT5 | P06229: 1exn 1j5f 1ut5 1ut8 5hml 5hmm 5hnk 5hp4

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