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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL INTRON-ENCODED HOMING ENDONUCLEASE I-TSP061I
 
Authors :  H. Nakayama, H. Tsuge, T. Shimamura, M. Miyano, N. Nomura, Y. Sako
Date :  06 Jan 06  (Deposition) - 06 Jul 06  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (1x)
Biol. Unit 2:  X  (3x)
Keywords :  Alpha/Beta Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nakayama, T. Shimamura, T. Imagawa, N. Shirai, T. Itoh, Y. Sako, M. Miyano, H. Sakuraba, T. Ohshima, N. Nomura, H. Tsuge
Structure Of A Hyperthermophilic Archaeal Homing Endonuclease, I-Tsp061I: Contribution Of Cross-Domain Polar Networks To Thermostability.
J. Mol. Biol. V. 365 362 2007
PubMed-ID: 17069851  |  Reference-DOI: 10.1016/J.JMB.2006.09.066

(-) Compounds

Molecule 1 - PUTATIVE HOMING ENDONUCLEASE
    Chains: X
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOPROTEUS
    Organism Taxid: 2270
    Strain: IC-061
    Synonym: ARCHAEAL INTRON-ENCODED DNA ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (1x): X
Biological Unit 2 (3x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR X:123 , ILE X:124 , TRP X:169 , LEU X:195 , HOH X:474BINDING SITE FOR RESIDUE CL X 201
2AC2SOFTWAREGLY X:-7 , LEU X:-6 , SER X:-8 , ARG X:125 , HOH X:356 , HOH X:358 , HOH X:375 , HOH X:384BINDING SITE FOR RESIDUE SO4 X 301
3AC3SOFTWARELYS X:2 , ARG X:152 , HOH X:306 , HOH X:404BINDING SITE FOR RESIDUE SO4 X 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DCH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DCH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DCH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DCH)

(-) Exons   (0, 0)

(no "Exon" information available for 2DCH)

(-) 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 X from PDB  Type:PROTEIN  Length:204
 aligned with Q8J309_9CREN | Q8J309 from UniProtKB/TrEMBL  Length:203

    Alignment length:207
                                1                                                                                                                                                                                                          
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       
         Q8J309_9CREN     - ----MRGGRKNMKVWDYLCGLIAADGHLDEEGYITISQKDRRFIDKIVALLKSAEIKISSLFYDKGAGVWKIKIKDERLYRYLVNNGVIPGKKAHVLRPPSSAVDPLWYIIGFIDGDGWVEQVVKRAGDKSYYYIRIGIKTKSKELRDWIAQTLNDLGIRASRADKSDGYEVHIDGVEAWRLVPHLQNPTHLERAQSVKDNRLSLLF 203
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhee....eeee...hhhhhhhhhhhhhhhh..eeeeeee....eeeeeeehhhhhhhhhh.......---.........hhhhhhhhhhhhhheeeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhhh....eeeee..eeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dch X -10 HSSGLVPRGSHMKVWDYLCGLIAADGHLDEEGYITILQKDRRFIDKIVALLKSAEIKISSLFYDKGAGVWKIKVKDERLYRYLVNNGVIPGK---VLRPPSSAVDPLWYIIGFIDGDGWVEQVVKRAGDKSYYYIRIGIKTKSKELRDWIAQTLNDLGIRASRADKSDGYEVHIDGVEAWRLVPHLQNPTHLERAQSVKDNRLSLLF 196
                                    -1         9        19        29        39        49        59        69        79 |   |  89        99       109       119       129       139       149       159       169       179       189       
                                                                                                                      81  85
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2DCH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DCH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DCH)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain X   (Q8J309_9CREN | Q8J309)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    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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