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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  I-DMOI, INTRON-ENCODED ENDONUCLEASE
 
Authors :  P. Van Roey, G. H. Silva
Date :  03 Dec 98  (Deposition) - 24 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Intron-Encoded, Endonuclease, Homing, Thermostable (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. H. Silva, J. Z. Dalgaard, M. Belfort, P. Van Roey
Crystal Structure Of The Thermostable Archaeal Intron-Encoded Endonuclease I-Dmoi.
J. Mol. Biol. V. 286 1123 1999
PubMed-ID: 10047486  |  Reference-DOI: 10.1006/JMBI.1998.2519
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (I-DMOI)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DL41(DE3)
    Expression System Taxid: 562
    Organism Scientific: DESULFUROCOCCUS MOBILIS
    Organism Taxid: 2274
    Other Details: SELENOMETHIONYL PROTEIN
    Other Details - Source: SELENOMETHIONINE AUXOTROPH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1B24)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B24)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B24)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B24)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_ENDONUCLEASEPS50819 Intein DOD-type homing endonuclease domain profile.DMO1_DESMO14-147  1A:14-147

(-) Exons   (0, 0)

(no "Exon" information available for 1B24)

(-) 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:173
 aligned with DMO1_DESMO | P21505 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   
           DMO1_DESMO     7 VSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILS 179
               SCOP domains d1b24a1 A:7-99 DNA endonuclease I-dmoI                                                       d1b24a2 A:100-179 DNA endonuclease I-dmoI                                        SCOP domains
               CATH domains 1b24A01 A:7-101 Homing endonucleases                                                           ---1b24A02 A:105-178 Homing endonucleases                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeeee.....eeeeeeeee..hhhhhh...hhhhhhhhh.......eeee....eeeeee.hhhhhhhh.....hhh....hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh...eeeeeee....eeeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------INTEIN_ENDONUCLEASE  PDB: A:14-147 UniProt: 14-147                                                                                    -------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b24 A   7 VSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLmQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANmLERIRLFNmREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILS 179
                                    16        26        36        46        56        66        76        86       |96      |106       116       126       136       146       156       166       176   
                                                                            56-MSE                                94-MSE  103-MSE
   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  (0, 0)

(no "Pfam Domain" information available for 1B24)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DMO1_DESMO | P21505)
molecular function
    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:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    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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  1b24
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMO1_DESMO | P21505: 1mow 2vs7 2vs8 4d6n 4d6o 4un7 4un8 4un9 4una 4unb 4unc 4ut0 5a0w 5ak9 5akf 5akm 5akn

(-) Related Entries Specified in the PDB File

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