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(-) Description

Title :  H98Q MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED WITH DNA
 
Authors :  J. H. Eastberg, B. L. Stoddard
Date :  07 Dec 06  (Deposition) - 30 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homing Endonuclease, Homodimer, Protein/Dna Complex, Hnh, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Eastberg, J. Eklund, R. Monnat, B. L. Stoddard
Mutability Of An Hnh Nuclease Imidazole General Base And Exchange Of A Deprotonation Mechanism.
Biochemistry V. 46 7215 2007
PubMed-ID: 17516660  |  Reference-DOI: 10.1021/BI700418D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTRON-ENCODED ENDONUCLEASE I-PPOI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-PPO
    Expression System Strain: BL21-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: I-PPOI
    Mutation: YES
    Organism Scientific: PHYSARUM POLYCEPHALUM
    Organism Taxid: 5791
    Synonym: I-PPO
 
Molecule 2 - 5'- D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP* DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'
    Chains: C, D
    Engineered: YES
    Other Details: I-PPOI BINDING SEQUENCE
    Synthetic: YES

 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
1MG2Ligand/IonMAGNESIUM ION
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:41 , CYS A:100 , CYS A:105 , HIS A:110BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWARECYS A:125 , CYS A:132 , HIS A:134 , CYS A:138BINDING SITE FOR RESIDUE ZN A 602
3AC3SOFTWARECYS B:325 , CYS B:332 , HIS B:334 , CYS B:338BINDING SITE FOR RESIDUE ZN B 603
4AC4SOFTWARECYS B:241 , CYS B:300 , CYS B:305 , HIS B:310BINDING SITE FOR RESIDUE ZN B 604
5AC5SOFTWAREASN B:319 , HOH B:701 , HOH B:702 , HOH B:703 , DA C:413 , DG C:414BINDING SITE FOR RESIDUE MG C 605
6AC6SOFTWAREASN A:119 , HOH A:704 , HOH A:705 , HOH A:706 , DA D:513 , DG D:514BINDING SITE FOR RESIDUE MG D 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O6M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:48 -Pro A:49
2Ala B:248 -Pro B:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O6M)

(-) Exons   (0, 0)

(no "Exon" information available for 2O6M)

(-) 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 d2o6ma_ A: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 2o6mA00 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..eeeeeeee..eeeeee..hhhhh....ee..ee.eeee........hhh.eeeehhhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o6m A   2 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASQLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 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 d2o6mb_ B: Intron-encoded homing endonuclease I-PpoI                                                                                                               SCOP domains
               CATH domains 2o6mB00 B:202-363 Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...........eeeee..eeeeeeee..eeeeee..hhhhh....ee..eeeeeee........hhh.eeeeehhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o6m B 202 ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASQLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV 363
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361  


Chain C from PDB  Type:DNA  Length:21
                                                     
                 2o6m C 401 TTGACTCTCTTAAGAGAGTCA 421
                                   410       420 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 2o6m D 501 TTGACTCTCTTAAGAGAGTCA 521
                                   510       520
   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  (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 2O6M)

(-) 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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  PPO1_PHYPO | Q94702
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  3.1.-.-
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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 1ipp

(-) Related Entries Specified in the PDB File

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