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(-) Description

Title :  MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
 
Authors :  P. Redondo, J. Prieto, I. G. Munoz, A. Alibes, F. Stricher, L. Serrano, S. Arnould, C. Perez, J. P. Cabaniols, P. Duchateau, F. Paques, F. J. Blanco, G. Montoya
Date :  14 Sep 07  (Deposition) - 28 Oct 08  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,E,S,T
Keywords :  Uv-Induced Dna Damage, Cutting Dna Endonucleases, Endonuclease, Intron Homing, Ini3- 4_magnesium, Plastid, Nuclease, Hydrolase, Chloroplast, Double Strand Break (Dsb), Homing Endonucleases (Hes) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Redondo, J. Prieto, I. G. Munoz, A. Alibes, F. Stricher, L. Serrano, J. P. Cabaniols, F. Daboussi, S. Arnould, C. Perez, P. Duchateau, F. Paques, F. J. Blanco, G. Montoya
Molecular Basis Of Xeroderma Pigmentosum Group C Dna Recognition By Engineered Meganucleases
Nature V. 456 107 2008
PubMed-ID: 18987743  |  Reference-DOI: 10.1038/NATURE07343

(-) Compounds

Molecule 1 - DNA ENDONUCLEASE I-CREI
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CDFDUET-1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Variant: D3PLYSS
    Fragment: RESIDUES 1-153
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Other Details: INI3 STREP-TAG C-TERM INI4 HIS-TAG C-TERM
    Synonym: 23S RRNA INTRON PROTEIN, INI3-4-MG
 
Molecule 2 - DNA ENDONUCLEASE I-CREI
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CDFDUET-1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Variant: D3PLYSS
    Fragment: RESIDUES 1-153
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Other Details: INI3 STREP-TAG C-TERM INI4 HIS-TAG C-TERM
    Synonym: 23S RRNA INTRON PROTEIN, INI3-4-MG
 
Molecule 3 - 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3'
    Chains: C
    Synthetic: YES
 
Molecule 4 - 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3'
    Chains: S
    Synthetic: YES
 
Molecule 5 - 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3'
    Chains: E
    Synthetic: YES
 
Molecule 6 - 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3'
    Chains: T
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCEST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , ASP B:20 , HOH B:2037 , DA E:14 , MG E:1025 , DA S:15 , HOH S:2004BINDING SITE FOR RESIDUE MG A1154
2AC2SOFTWAREGLY A:19 , ASP A:20 , MG A:1154 , GLY B:19 , ASP B:20 , DA C:14 , DA E:14 , MG E:1026 , DA S:15 , DA T:15BINDING SITE FOR RESIDUE MG E1025
3AC3SOFTWAREASP A:20 , GLY B:19 , HOH B:2014 , DA C:14 , MG E:1025 , DA T:15 , HOH T:2002BINDING SITE FOR RESIDUE MG E1026
4AC4SOFTWAREALA A:134 , ASN A:136 , HOH A:2095 , HOH A:2096 , HOH A:2099 , HOH A:2100 , HOH B:2048BINDING SITE FOR RESIDUE CA A1155
5AC5SOFTWAREALA B:134 , ASN B:136 , HOH B:2108 , HOH B:2109 , HOH B:2112 , HOH B:2113 , HOH B:2115BINDING SITE FOR RESIDUE CA B1154

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VBN)

(-) 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:153
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           DNE1_CHLRE     1 MNTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
               SCOP domains d2vbna_ A: automated matches                                                                                                                              SCOP domains
               CATH domains 2vbnA00 A:1-153 Homing endonucleases                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee..eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vbn A   1 MNTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSSKFKHRLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDSGSVSNYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with DNE1_CHLRE | P05725 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           DNE1_CHLRE     2 NTKYNKEFLLYLAGFVDGDGSIIAQIKPNQSYKFKHQLSLTFQVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
               SCOP domains d2vbnb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains 2vbnB00 B:2-153 Homing endonucleases                                                                                                                     CATH domains
           Pfam domains (1) -----------LAGLIDADG_1-2vbnB01 B:13-109                                                                     -------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------LAGLIDADG_1-2vbnB02 B:13-109                                                                     -------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee...eeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vbn B   2 NTKYNKEFLLYLAGFVDGDGSIIAQIEPNQSYKFKHRLKLTFKVTQKTQRRWFLDKLVDEIGVGYVSDSGSVSNYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  


Chain C from PDB  Type:DNA  Length:14
                                              
                 2vbn C   1 TTAGGATCCTTCAA  14
                                    10    


Chain E from PDB  Type:DNA  Length:14
                                              
                 2vbn E   1 TCTGCCTTTTTTGA  14
                                    10    


Chain S from PDB  Type:DNA  Length:10
                                          
                 2vbn S  15 AAAAGGCAGA  24
                                    24


Chain T from PDB  Type:DNA  Length:10
                                          
                 2vbn T  15 AGGATCCTAA  24
                                    24
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DNE1_CHLRE | P05725)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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  2vbn
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNE1_CHLRE | P05725: 1af5 1bp7 1g9y 1g9z 1mow 1n3e 1n3f 1t9i 1t9j 1u0c 1u0d 2i3p 2i3q 2o7m 2vbj 2vbl 2vbo 4aab 4aad 4aae 4aaf 4aag 4aqu 4aqx

(-) Related Entries Specified in the PDB File

1af5 GROUP I MOBILE INTRON ENDONUCLEASE
1bp7 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DEOXYRIBONUCLEIC ACID
1g9y HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITHCALCIUM
1g9z LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEXWITH MAGNESIUM
1mow E-DREI
1n3e CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE I (PALINDROME OF LEFT SIDE OF WILDTYPE DNA TARGETSEQUENCE)
1n3f CRYSTAL STRUCTURE OF I-CREI BOUND TO A PALINDROMIC DNASEQUENCE II (PALINDROME OF RIGHT SIDE OF WILDTYPE DNATARGET SEQUENCE)
1t9i I-CREI(D20N)/DNA COMPLEX
1t9j I-CREI(Q47E)/DNA COMPLEX
1u0c Y33C MUTATANT OF HOMING ENDONUCLEASE I-CREI
1u0d Y33H MUTATANT OF HOMING ENDONUCLEASE I-CREI
2vbj MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
2vbl MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS
2vbo MOLECULAR BASIS OF HUMAN XPC GENE RECOGNITION AND CLEAVAGE BY ENGINEERED HOMING ENDONUCLEASE HETERODIMERS