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(-) Description

Title :  DNA BINDING AND CLEAVAGE BY THE HNH HOMING ENDONUCLEASE I-HMUI
 
Authors :  B. W. Shen, M. Landthaler, D. A. Shub, B. L. Stoddard
Date :  21 Jul 04  (Deposition) - 31 Aug 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym./Biol. Unit :  A,B,C,M
Keywords :  Hnh Catalytic Motif, Helix-Turn-Helix Dna Binding Domain, Protein-Dna Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Shen, M. Landthaler, D. A. Shub, B. L. Stoddard
Dna Binding And Cleavage By The Hnh Homing Endonuclease I-Hmui.
J. Mol. Biol. V. 342 43 2004
PubMed-ID: 15313606  |  Reference-DOI: 10.1016/J.JMB.2004.07.032

(-) Compounds

Molecule 1 - 36-MER
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP *AP*GP*C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - HNH HOMING ENDONUCLEASE
    Chains: M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKYB1
    Expression System Strain: BL21(DE3)CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BACTERIOPHAGE SP01
    Organism Scientific: BACILLUS PHAGE SPO1
    Organism Taxid: 10685

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MN1Ligand/IonMANGANESE (II) ION
3SR4Ligand/IonSTRONTIUM ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDC B:22 , DG C:23 , ASP M:74 , ASN M:96 , HOH M:420 , HOH M:421BINDING SITE FOR RESIDUE MN M 413
02AC2SOFTWAREEDO B:403BINDING SITE FOR RESIDUE SR A 414
03AC3SOFTWAREHOH B:405BINDING SITE FOR RESIDUE SR A 415
04AC4SOFTWARELYS M:118 , GLN M:120 , SR M:418BINDING SITE FOR RESIDUE SR M 417
05AC5SOFTWAREHOH B:404 , LYS M:118 , SR M:417BINDING SITE FOR RESIDUE SR M 418
06AC6SOFTWAREDG C:27 , DG C:28 , GLY M:50 , THR M:52BINDING SITE FOR RESIDUE EDO C 397
07AC7SOFTWAREDT B:8 , ARG M:160 , ILE M:161 , HIS M:162BINDING SITE FOR RESIDUE EDO M 398
08AC8SOFTWAREPRO M:128 , HOH M:427BINDING SITE FOR RESIDUE EDO M 399
09AC9SOFTWARELYS M:7 , HIS M:62 , CYS M:64 , GLU M:65 , GLU M:134BINDING SITE FOR RESIDUE EDO M 400
10BC1SOFTWAREDA A:20 , DG A:21 , HOH A:416 , DG B:16BINDING SITE FOR RESIDUE EDO A 401
11BC2SOFTWAREDC A:27 , DC A:28 , SR A:414 , DA B:12 , DA B:13BINDING SITE FOR RESIDUE EDO B 403
12BC3SOFTWARETRP M:3 , GLN M:14 , ASP M:129 , HOH M:430 , HOH M:432BINDING SITE FOR RESIDUE TRS M 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U3E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U3E)

(-) Exons   (0, 0)

(no "Exon" information available for 1U3E)

(-) 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:DNA  Length:36
                                                                    
                 1u3e A   2 GTAATGAGCCTAACGCTCAGCAATTCCCACGTAAGA  37
                                    11        21        31      


Chain B from PDB  Type:DNA  Length:21
                                                     
                 1u3e B   2 CTTACGTGGGAATTGCTGAGC  22
                                    11        21 


Chain C from PDB  Type:DNA  Length:15
                                               
                 1u3e C  23 GTTAGGCTCATTACT  37
                                    32     


Chain M from PDB  Type:PROTEIN  Length:174
 aligned with HMUI_BPSP1 | P34081 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           HMUI_BPSP1     1 MEWKDIKGYEGHYQVSNTGEVYSIKSGKTLKHQIPKDGYHRIGLFKGGKGKTFQVHRLVAIHFCEGYEEGLVVDHKDGNKDNNLSTNLRWVTQKINVENQMSRGTLNVSKAQQIAKIKNQKPIIVISPDGIEKEYPSTKCACEELGLTRGKVTDVLKGHRIHHKGYTFRYKLNG 174
               SCOP domains d1u3em1 M:1-105 Intron-encoded homing endonuclease I-HmuI                                                d1u3em2 M:106-174 Intron-encoded homing endonuclease I-HmuI           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------1u3eM02 M:107-174 'winged helix' repressor DNA binding domain        CATH domains
               Pfam domains NUMOD4-1u3eM02 M:1-47                          -----HNH_3-1u3eM01 M:53-98                         ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......eeee....eee.....ee..........eeeeee..eeeeeehhhhhhhhhh.......eeee........hhh.eeeehhhhhhhhhhhhh...hhhhhhhhhhhh...eeee.....eeee.hhhhhhhhhh.hhhhhhhhhh.........eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u3e M   1 MEWKDIKGYEGHYQVSNTGEVYSIKSGKTLKHQIPKDGYHRIGLFKGGKGKTFQVHRLVAIHFCEGYEEGLVVDHKDGNKDNNLSTNLRWVTQKINVENQMSRGTLNVSKAQQIAKIKNQKPIIVISPDGIEKEYPSTKCACEELGLTRGKVTDVLKGHRIHHKGYTFRYKLNG 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)
(-)
Clan: no clan defined [family: NUMOD4] (1)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain M   (HMUI_BPSP1 | P34081)
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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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

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(-) Related Entries Specified in the PDB File

1a73 INTRON-ENCODED ENDONUCLEASE I-PPO1 COMPLEXED WITH DNA (HIS- CYS BOX)
1fsj CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN (NON-SPECIFIC HNH NUCLEASE)
1i3j DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH SUBSTRATE
1pt3 CRYSTAL STRUCTURE OF NUCLEASE-COLE& COMPLEXED WITH OCTAMER DNA (NON-SPECIFIC HNH NUCLEASE)