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(-) Description

Title :  CRYSTAL STRUCTURE OF A RESTRICTION ENZYME PABI IN COMPLEX WITH DNA
 
Authors :  K. Miyazono, T. Miyakawa, T. Ito, M. Tanokura
Date :  10 May 13  (Deposition) - 29 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Enzyme, Dna Binding, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyazono, Y. Furuta, M. Watanabe-Matsui, T. Miyakawa, T. Ito, I. Kobayashi, M. Tanokura
A Sequence-Specific Dna Glycosylase Mediates Restriction-Modification In Pyrococcus Abyssi
Nat Commun 2014
PubMed: search  |  Reference-DOI: 10.1038/NCOMMS4178

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 8-226
    Gene: PYRAB01580, PAB0105
    Mutation: YES
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 272844
    Strain: GE5
    Synonym: RESTRICTION ENZYME PABI
 
Molecule 2 - DNA (5'-D(*GP*CP*AP*TP*AP*GP*CP*TP*GP*TP*(ORP) P*CP*AP*GP*CP*TP*AP*TP*GP*C)-3')
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHESIZED OLIGONULEOTIDE CONTAINING A PABI RECOGNITION SEQUENCE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2ORP2Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , ILE A:66 , TYR A:68 , SER A:162 , MET A:163 , VAL A:164 , PHE A:204 , HIS A:211 , DT D:10 , ORP D:11BINDING SITE FOR RESIDUE ADE A 301
2AC2SOFTWAREGLN B:65 , ILE B:66 , TYR B:68 , SER B:162 , MET B:163 , VAL B:164 , PHE B:204 , HIS B:211 , DT C:10BINDING SITE FOR RESIDUE ADE B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WAZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:174 -Pro A:175
2Glu B:174 -Pro B:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WAZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WAZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WAZ)

(-) 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:216
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:216
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      
         Q9V2B6_PYRAB     8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eeeeeee.......eeeeeee..eeee..........hhhhh.eeeee............hhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhh..eeeeeeeee..eeeeeeeeeeeeee.....eeeeeeee......eeeeeeeeee.................eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3waz A   8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHAQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:217
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
         Q9V2B6_PYRAB     8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSIIG 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeeeee.......eeeeeee..eeee..........hhhhh.eeeee............hhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhh..eeeeeeeee..eeeeeeeeeeeeee.....eeeeeeee......eeeeeeeeee.hhh.............eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3waz B   8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHAQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSIIG 224
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       


Chain C from PDB  Type:DNA  Length:20
                                                    
                 3waz C   1 GCATAGCTGTxCAGCTATGC  20
                                    10|       20
                                     11-ORP     


Chain D from PDB  Type:DNA  Length:20
                                                    
                 3waz D   1 GCATAGCTGTxCAGCTATGC  20
                                    10|       20
                                     11-ORP
   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  (0, 0)

(no "SCOP Domain" information available for 3WAZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WAZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WAZ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WAZ)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9V2B6_PYRAB | Q9V2B6: 2dvy 5iff

(-) Related Entries Specified in the PDB File

2dvy