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(-) Description

Title :  HOMING ENDONUCLEASE/DNA COMPLEX
 
Authors :  K. E. Flick, M. S. Jurica, R. J. Monnat Jr. , B. L. Stoddard
Date :  19 Mar 98  (Deposition) - 02 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homing Endonuclease, Intron, Zinc, Dna Binding, Protein Folding, Transcription/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Flick, M. S. Jurica, R. J. Monnat Jr. , B. L. Stoddard
Dna Binding And Cleavage By The Nuclear Intron-Encoded Homing Endonuclease I-Ppoi.
Nature V. 394 96 1998
PubMed-ID: 9665136  |  Reference-DOI: 10.1038/27952
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP *CP*A)-3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - INTRON-ENCODED ENDONUCLEASE I-PPOI
    Cellular Location: NUCLEUS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PHYSARUM POLYCEPHALUM
    Organism Taxid: 5791

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:125 , CYS A:132 , HIS A:134 , CYS A:138 , HOH A:457BINDING SITE FOR RESIDUE CD A 301
2AC2SOFTWARECYS A:41 , CYS A:100 , CYS A:105 , HIS A:110BINDING SITE FOR RESIDUE CD A 302
3AC3SOFTWAREASN A:119 , HOH A:306 , HOH A:307 , HOH A:308 , DA D:213 , HOH D:222BINDING SITE FOR RESIDUE MG A 305
4AC4SOFTWARECYS B:125 , CYS B:132 , HIS B:134 , CYS B:138BINDING SITE FOR RESIDUE CD B 303
5AC5SOFTWARECYS B:41 , CYS B:100 , CYS B:105 , HIS B:110BINDING SITE FOR RESIDUE CD B 304
6AC6SOFTWAREASN B:119 , HOH B:307 , HOH B:308 , HOH B:309 , DA C:213 , HOH C:222BINDING SITE FOR RESIDUE MG B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:48 -Pro A:49
2Ala B:48 -Pro B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IPP)

(-) 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:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1ippa_ A: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1ippA00 A:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee...........eeeee..eeeeeee....eeeee...hhh.....ee..ee.eeee.........hhheeee.hhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ipp A   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with PPO1_PHYPO | Q94702 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           PPO1_PHYPO     2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
               SCOP domains d1ippb_ B: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 1ippB00 B:2-163 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee...........eeeee..eeeeeee....eeeee...hhh.....ee..ee.eeee.........hhheeee.hhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ipp B   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain C from PDB  Type:DNA  Length:21
                                                     
                 1ipp C 201 TTGACTCTCTTAAGAGAGTCA 221
                                   210       220 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 1ipp D 201 TTGACTCTCTTAAGAGAGTCA 221
                                   210       220
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1IPP)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPO1_PHYPO | Q94702)
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: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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  1ipp
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  PPO1_PHYPO | Q94702
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPO1_PHYPO | Q94702: 1a73 1a74 1cyq 1cz0 1evw 1evx 2o6m

(-) Related Entries Specified in the PDB File

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