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(-) Description

Title :  STRUCTURE OF THE CATALYTIC DOMAIN OF HOMING ENDONUCLEASE I-TEVI
 
Authors :  P. Van Roey, L. Meehan, J. C. Kowalski, M. Belfort, V. Derbyshire
Date :  02 May 02  (Deposition) - 30 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Van Roey, L. Meehan, J. C. Kowalski, M. Belfort, V. Derbyshire
Catalytic Domain Structure And Hypothesis For Function Of Giy-Yig Intron Endonuclease I-Tevi.
Nat. Struct. Biol. V. 9 806 2002
PubMed-ID: 12379841
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTRON-ASSOCIATED ENDONUCLEASE 1
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN (RESIDUES 1 TO 97)
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: HOMING ENDONUCLEASE I-TEVI, IRF PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:242 , ASN B:10 , ASN B:13 , LYS B:15 , SER B:48 , HIS B:52 , TYR B:89BINDING SITE FOR RESIDUE SO4 B 502
2AC2SOFTWAREASN A:10 , ASN A:13 , LYS A:15 , SER A:48 , HIS A:52 , TYR A:89 , HOH A:233 , HOH A:313 , HOH A:338 , HOH A:380 , HOH B:210BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:39 -B:39

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LN0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LN0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIY_YIGPS50164 GIY-YIG domain profile.TEV1_BPT41-88  1B:1-88

(-) Exons   (0, 0)

(no "Exon" information available for 1LN0)

(-) 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:92
 aligned with TEV1_BPT4 | P13299 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:92
                                    11        21        31        41        51        61        71        81        91  
             TEV1_BPT4    2 KSGIYQIKNTLNNKVYVGSAKDFEKRWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECSILEEIPYEKDLIIERENFWIKELNSKINGYNIAD 93
               SCOP domains d1ln0a_ A: Homing endonuclease I-TevI                                                        SCOP domains
               CATH domains 1ln0A00 A:2-93 GIY-YIG endonuclease                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GIY_YIG  PDB: - UniProt: 1-88                                                          ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  1ln0 A  2 KSGIYQIKNTLNNKVYVGSAKDFEKAWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECSILEEIPYEKDLIIERENFWIKELNSKINGYNIAD 93
                                    11        21        31        41        51        61        71        81        91  


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with TEV1_BPT4 | P13299 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
             TEV1_BPT4    1 MKSGIYQIKNTLNNKVYVGSAKDFEKRWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECSILEEIPYEKDLIIERENFWIKELNSKINGYNIADA 94
               SCOP domains d1ln0b_ B: Homing endonuclease I-TevI                                                          SCOP domains
               CATH domains 1ln0B00 B:1-94 GIY-YIG endonuclease                                                            CATH domains
           Pfam domains (1) -GIY-YIG-1ln0B01 B:2-90                                                                   ---- Pfam domains (1)
           Pfam domains (2) -GIY-YIG-1ln0B02 B:2-90                                                                   ---- Pfam domains (2)
         Sec.struct. author ...eeeeeee.....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GIY_YIG  PDB: B:1-88 UniProt: 1-88                                                      ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  1ln0 B  1 MKSGIYQIKNTLNNKVYVGSAKDFEKAWKRHFKDLEKGCHSSIKLQRSFNKHGNVFECSILEEIPYEKDLIIERENFWIKELNSKINGYNIADA 94
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GIY-YIG (10)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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: 1i3j 1mk0 1t2t

(-) Related Entries Specified in the PDB File

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