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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE
 
Authors :  P. Van Roey, C. A. Waddling, K. M. Fox, M. Belfort, V. Derbyshire
Date :  15 Feb 01  (Deposition) - 13 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Extended Structure, Zn-Finger, Minor Groove Helix, Helix-Turn-Helix, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Van Roey, C. A. Waddling, K. M. Fox, M. Belfort, V. Derbyshire
Intertwined Structure Of The Dna-Binding Domain Of Intron Endonuclease I-Tevi With Its Substrate.
Embo J. V. 20 3631 2001
PubMed-ID: 11447104  |  Reference-DOI: 10.1093/EMBOJ/20.14.3631
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP *AP*T)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP *GP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - INTRON-ASSOCIATED ENDONUCLEASE 1
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: I-TEVI

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:151 , CYS A:153 , CYS A:164 , CYS A:167BINDING SITE FOR RESIDUE ZN A 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I3J)

(-) Exons   (0, 0)

(no "Exon" information available for 1I3J)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:96
 aligned with TEV1_BPT4 | P13299 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:96
                                   158       168       178       188       198       208       218       228       238      
            TEV1_BPT4   149 KFCKCGVRIQTSAYTCSKCRNRSGENNSFFNHKHSDITKSKISEKMKGKKPSNIKKISCDGVIFDCAADAARHFKISSGLVTYRVKSDKWNWFYIN 244
               SCOP domains d1i3ja_ A: DNA-binding domain of intron endonuclease I-TevI                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................hhhhh.......hhhhhhhhhhhhh.........eee..eee.hhhhhhhhhh.hhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1i3j A 149 KFCKCGVRIQTSAYTCSKCRNRSGENNSFFNHKHSDITKSKISEKMKGKKPSNIKKISCDGVIFDCAADAARHFKISSGLVTYRVKSDKWNWFYIN 244
                                   158       168       178       188       198       208       218       228       238      


Chain B from PDB  Type:DNA  Length:21
                                                     
                 1i3j B   1 TTCTTGGGTCTACCGTTTAAT  21
                                    10        20 


Chain C from PDB  Type:DNA  Length:21
                                                     
                 1i3j C  31 AATTAAACGGTAGACCCAAGA  51
                                    40        50
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1I3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I3J)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TEV1_BPT4 | P13299)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TEV1_BPT4 | P13299: 1ln0 1mk0 1t2t

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