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(-) Description

Title :  DIVALENT METAL IONS (MANGANESE) BOUND TO T5 5'-EXONUCLEASE
 
Authors :  T. A. Ceska, J. R. Sayers, D. Suck
Date :  04 Dec 03  (Deposition) - 05 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Exonuclease, Nuclease, 3D-Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Feng, D. Patel, J. Dervan, T. A. Ceska, D. Suck, I. Haq, J. R. Sayers
Roles Of Divalent Metal Ions In Flap Endonuclease-Substrate Interactions
Nat. Struct. Mol. Biol. V. 11 450 2004
PubMed-ID: 15077103  |  Reference-DOI: 10.1038/NSMB754

(-) Compounds

Molecule 1 - EXODEOXYRIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACTERIOPHAGE T5
    Organism Taxid: 10726
    Synonym: 5'-EXONUCLEASE

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:128 , ASP A:130 , HOH A:2110 , HOH A:2111BINDING SITE FOR RESIDUE MN A1291
2AC2SOFTWAREASP A:155 , ASP A:201 , HOH A:2084 , HOH A:2085BINDING SITE FOR RESIDUE MN A1292
3AC3SOFTWAREASP B:68 , ASP B:130 , HOH B:2062BINDING SITE FOR RESIDUE MN B1292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UT5)

(-) 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 1UT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UT5)

(-) Exons   (0, 0)

(no "Exon" information available for 1UT5)

(-) 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:272
 aligned with EXO5_BPT5 | P06229 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:272
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
            EXO5_BPT5    20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
               SCOP domains d1ut5a2 A:20-185 T5 5'-exonuclease                                                                                                                                    d1ut5a1 A:186-291 T5 5'-exonuclease                                                                        SCOP domains
               CATH domains 1ut5A02 A:20-179,A:261-286 5'-nuclease                                                                                                                          -1ut5A01 A:181-260 5' to 3' exonuclease, C-terminal subdomain                    1ut5A02 A:20-179,A:261-286----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhhhhhhhh..eeee..hhhhhhhh....eeee....eee...hhhhhhh..hhhhhhhhhhhhh............hhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ut5 A  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with EXO5_BPT5 | P06229 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:272
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
            EXO5_BPT5    20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
               SCOP domains d1ut5b2 B:20-185 T5 5'-exonuclease                                                                                                                                    d1ut5b1 B:186-291 T5 5'-exonuclease                                                                        SCOP domains
               CATH domains 1ut5B02 B:20-179,B:261-286 5'-nuclease                                                                                                                          -1ut5B01 B:181-260 5' to 3' exonuclease, C-terminal subdomain                    1ut5B02 B:20-179,B:261-286----- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------5_3_exonuc-1ut5B01 B:188-274                                                           ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------5_3_exonuc-1ut5B02 B:188-274                                                           ----------------- Pfam domains (2)
           Pfam domains (3) 5_3_exonuc_N-1ut5B03 B:20-188                                                                                                                                            ------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) 5_3_exonuc_N-1ut5B04 B:20-188                                                                                                                                            ------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhh...eeeee....eeehhhhhhhhhh..hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ut5 B  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
   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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 Related Entries

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

UniProtKB/Swiss-Prot
        EXO5_BPT5 | P06229: 1exn 1j5f 1ut8 1xo1 5hml 5hmm 5hnk 5hp4

(-) Related Entries Specified in the PDB File

1exn T5 5'-EXONUCLEASE
1j5f REVISED MODEL OF T5 5' NUCLEASE + DNA
1ut8 DIVALENT METAL IONS (ZINC) BOUND TO T5 5 '-EXONUCLEASE
1xo1 T5 5'-EXONUCLEASE MUTANT K83A