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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BETA-BETA-ALPHA-ME TYPE II RESTRICTION ENDONUCLEASE HPY99I
 
Authors :  M. Sokolowska, H. Czapinska, M. Bochtler
Date :  21 Nov 08  (Deposition) - 31 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Hpy99I, Pseudopalindrome, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sokolowska, H. Czapinska, M. Bochtler
Crystal Structure Of The Beta Beta Alpha-Me Type Ii Restriction Endonuclease Hpy99I With Target Dna.
Nucleic Acids Res. V. 37 3799 2009
PubMed-ID: 19380375  |  Reference-DOI: 10.1093/NAR/GKP228
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE HPY99I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15BMOD
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: JHP_0755, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85963
    Strain: J99
 
Molecule 2 - 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 3 - 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:68 , CYS A:71 , CYS A:97 , CYS A:100BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS A:130 , CYS A:133 , CYS A:161 , CYS A:164BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREASP A:148 , ASN A:165 , HOH A:439 , HOH A:516 , DG C:2 , DT C:3 , DG D:2 , DA D:3BINDING SITE FOR RESIDUE NA A 305
4AC4SOFTWAREASN A:12 , ILE A:54 , ASP A:55 , ARG A:58 , HOH A:196BINDING SITE FOR RESIDUE PG4 A 400
5AC5SOFTWARECYS B:68 , CYS B:71 , CYS B:97 , CYS B:100BINDING SITE FOR RESIDUE ZN B 303
6AC6SOFTWARECYS B:130 , CYS B:133 , CYS B:161 , CYS B:164BINDING SITE FOR RESIDUE ZN B 304
7AC7SOFTWAREASP B:148 , ASN B:165 , HOH B:208 , HOH B:466 , DG C:2 , DT C:3 , DG D:2 , DA D:3BINDING SITE FOR RESIDUE NA B 306
8AC8SOFTWAREASN B:12 , TYR B:57 , TYR B:63 , HOH B:198BINDING SITE FOR RESIDUE NA B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FC3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FC3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FC3)

(-) Exons   (0, 0)

(no "Exon" information available for 3FC3)

(-) 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:189
 aligned with Q9ZL26_HELPJ | Q9ZL26 from UniProtKB/TrEMBL  Length:190

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         Q9ZL26_HELPJ     1 MLKNDDFVIAKNQLGNIVPNSVGVIRAVNGKSAMVLFIGLNELKRVDFSELEAIDIYRTGKGYDKKICNICHILKNTDGFEINQTDAKGRKTTRPSCRECRKNIDGVKLSSTEKKKMDEIAPPKGSVFTCPICEKRSIVGVTANLVHDHNHDTGWGREWICDSCNTGLGRFKDNPKFLEKVIEYLKKYE 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...........eeeeeeee..eeeeee....eeeeee...eee.hhhhh.....eee......eee.hhh.eeee.....eee...hhhhhhhhhh...hhhhhhhhhhh......eee......eee......eeeee......eeeeeehhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fc3 A   1 MLKNDDFVIAKNQLGNIVPNSVGVIRAVNGKSAMVLFIGLNELKRVDFSELEAIDIYRTGKGYDKKICNICHILKNTDGFEINQTDAKGRKTTRPSCRECRKNIDGVKLSSTEKKKMDEIAPPKGSVFTCPICEKRSIVGVTANLVHDHNHDTGWGREWICDSCNTGLGRFKDNPKFLEKVIEYLKKYE 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q9ZL26_HELPJ | Q9ZL26 from UniProtKB/TrEMBL  Length:190

    Alignment length:188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
         Q9ZL26_HELPJ     2 LKNDDFVIAKNQLGNIVPNSVGVIRAVNGKSAMVLFIGLNELKRVDFSELEAIDIYRTGKGYDKKICNICHILKNTDGFEINQTDAKGRKTTRPSCRECRKNIDGVKLSSTEKKKMDEIAPPKGSVFTCPICEKRSIVGVTANLVHDHNHDTGWGREWICDSCNTGLGRFKDNPKFLEKVIEYLKKYE 189
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...........eeeeeee...eeeeee....eeeeee...eee.hhhhh.....eee......eee.hhh.eeee.....eee...hhhhhhhhhh...hhhhhhhhhh.......eee......eee......eeeee......eeeeeehhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fc3 B   2 LKNDDFVIAKNQLGNIVPNSVGVIRAVNGKSAMVLFIGLNELKRVDFSELEAIDIYRTGKGYDKKICNICHILKNTDGFEINQTDAKGRKTTRPSCRECRKNIDGVKLSSTEKKKMDEIAPPKGSVFTCPICEKRSIVGVTANLVHDHNHDTGWGREWICDSCNTGLGRFKDNPKFLEKVIEYLKKYE 189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        


Chain C from PDB  Type:DNA  Length:9
                                         
                 3fc3 C  -4 CTCGACGTA   4


Chain D from PDB  Type:DNA  Length:9
                                         
                 3fc3 D  -4 TACGTCGAG   4
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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 3FC3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FC3)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9ZL26_HELPJ | Q9ZL26)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3fc3
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        Q9ZL26_HELPJ | Q9ZL26: 3gox

(-) Related Entries Specified in the PDB File

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