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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASES PABI
 
Authors :  K. Miyazono, M. Watanabe, M. Kamo, T. Sawasaki, K. Nagata, Y. Endo, M. Tanokura, I. Kobayashi
Date :  01 Aug 06  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A,B,C,D  (1x)
Keywords :  Restriction Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyazono, M. Watanabe, J. Kosinski, K. Ishikawa, M. Kamo, T. Sawasaki, K. Nagata, J. M. Bujnicki, Y. Endo, M. Tanokura, I. Kobayashi
Novel Protein Fold Discovered In The Pabi Family Of Restriction Enzymes
Nucleic Acids Res. V. 35 1908 2007
PubMed-ID: 17332011  |  Reference-DOI: 10.1093/NAR/GKM091
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE PABI
    Chains: A, B, C, D, E, F
    Engineered: YES
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Other Details: WHEAT-GERM-BASED CELL-FREE PROTEIN SYNTHESIS SYSTEM

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF
Biological Unit 4 (1x): ABCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DVY)

(-) Sites  (0, 0)

(no "Site" information available for 2DVY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:174 -Pro A:175
2Glu B:174 -Pro B:175
3Glu C:174 -Pro C:175
4Glu D:174 -Pro D:175
5Glu E:174 -Pro E:175
6Glu F:174 -Pro F:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DVY)

(-) Sequences/Alignments

Asymmetric 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:223
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q9V2B6_PYRAB     1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eeeeee.........eeee....eee............hhh.eeeee...........hhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh.eeeeeeeee..eeeeeeeeeeeeee.....eeeee............eeeeeee.hhh.............eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvy A   1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
         Q9V2B6_PYRAB     7 VEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSIIGT 225
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeee........eeeeee....eee................eeeee............hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhh..eee....ee..eeeeeeeeeeee..........eeee.----...eeee.eeee.hhh..............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvy B   7 VEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKH----VGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSIIGT 225
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      |  - |     166       176       186       196       206       216         
                                                                                                                                                                            153  158                                                                   


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q9V2B6_PYRAB     1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeee.......eeeee.hhhh.ee............hhh.eeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhh.eee....ee..eeeeeeeeee.........eeeeeee.-----..eeeeeeeee.hhh.............eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvy C   1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKH-----GYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  |    160       170       180       190       200       210       220   
                                                                                                                                                                                  153   159                                                                


Chain D from PDB  Type:PROTEIN  Length:214
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:214
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217    
         Q9V2B6_PYRAB     8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRS 221
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......eeee........eeeee......ee................eeeee............hhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhh.eeeeeeeee..eeeeeeeeeee...........eeeee......eeeee..eee...ee.............eeee..hhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvy D   8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRS 221
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217    


Chain E from PDB  Type:PROTEIN  Length:223
 aligned with Q9V2B6_PYRAB | Q9V2B6 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q9V2B6_PYRAB     1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eeeee........eeeeee....eee................eeeee............hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeee........eeeeeeeeeeeee.....eeeeeeee......eeeeeeeeee.hhh..............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvy E   1 MIHLTSVEASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLKHKQRAVGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   


Chain F from PDB  Type:PROTEIN  Length:211
 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 ..eee......eeee........eeeeee....eee.........hhhhh..eeeee...........hhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhh.eee....ee..eeeeeeeeeeee.......eeeeeee-----...eeeeeee.hhh.ee.............eeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dvy F   8 EASVSFENGKIVVRLPITRPTSKIRVKKIENGVGIPVSTRKKSFPSDENLRDYYIEWQISYARDGKYDYELSRMVRLAHEHGILTYNDIYELLKFADDVKSYLEDKGIRRESTNEELYGFNIYEDVYPVAKKELPSGEFIGIVLK-----VGYQSMVYVCIPLTNVEPSLAGRVARRNEVVKYEVPVDLMKELLKAFIIASETHKNDIVKFLRSII 223
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147    |    -|      167       177       187       197       207       217      
                                                                                                                                                                          152   158
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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  (0, 0)

(no "SCOP Domain" information available for 2DVY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DVY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DVY)

(-) Gene Ontology  (0, 0)

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  Cis Peptide Bonds
    Glu A:174 - Pro A:175   [ RasMol ]  
    Glu B:174 - Pro B:175   [ RasMol ]  
    Glu C:174 - Pro C:175   [ RasMol ]  
    Glu D:174 - Pro D:175   [ RasMol ]  
    Glu E:174 - Pro E:175   [ RasMol ]  
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 Related Entries

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        Q9V2B6_PYRAB | Q9V2B6: 3waz 5iff

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