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(-) Description

Title :  RESTRICTION ENDONUCLEASE PSPGI-SUBSTRATE DNA COMPLEX
 
Authors :  R. H. Szczepanowski, M. Carpenter, H. Czapinska, G. Tamulaitis, V. Sik A. Bhagwat, M. Bochtler
Date :  12 Dec 07  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Endonuclease-Dna Complex, Restriction Enzyme, Pspgi, Base Flipping, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. H. Szczepanowski, M. Carpenter, H. Czapinska, G. Tamulaitis, V. Siksnys, A. Bhagwat, M. Bochtler
A Direct Crystallographic Demonstration That Type Ii Restriction Endonuclease Pspgi Flips Nucleotides
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PSPGI RESTRICTION ENDONUCLEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PYROCOCCUS SP. GI-H
    Organism Taxid: 83521
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:210 , ARG B:211 , GLN B:241 , LYS B:242 , HOH B:289 , HOH B:330 , HOH B:334 , HOH B:383BINDING SITE FOR RESIDUE CIT B 273

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BM3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:141 -Pro A:142
2Ile B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BM3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BM3)

(-) Exons   (0, 0)

(no "Exon" information available for 3BM3)

(-) 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:259
 aligned with O93646_9EURY | O93646 from UniProtKB/TrEMBL  Length:272

    Alignment length:259
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         
         O93646_9EURY     2 VRNLVIDITKKPTQNIPPTNEIIEEAITELNVDELLDRLFEKDESGEVITPSRIAKMLEEKAFEIYKEYEKQVREAYLSAGYSREKLEQSFQQARFSRGGKAFEIIFTKLLNKFGIRYEHDRVIKIYDYITEGEKPDFIIPSVRAFLNDPSSAILITVKRKVRERWREAVGEAQILRNKFGDEINFWFVGFDEEFTIYSAIAMLDNGIDRVYVIDGRYDSLIEEIKRISDPNFNEDKYIQKIRRFSDIFDDIIQFLNKH 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.......ee...eee.hhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhh......hhhhhhh.eee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bm3 A   2 VRNLVIDITKKPTQNIPPTNEIIEEAITELNVDELLDRLFEKDESGEVITPSRIAKmLEEKAFEIYKEYEKQVREAYLSAGYSREKLEQSFQQARFSRGGKAFEIIFTKLLNKFGIRYEHDRVIKIYDYITEGEKPAFIIPSVRTFLNDPSSAILITVKRKVRERWREAVGEAQILRNKFGDEINFWFVGFDEEFTIYSAIAmLDNGIDRVYVIDGRYDSLIEEIKRISDPNFNEDKYIQKIRRFSDIFDDIIQFLNKH 260
                                    11        21        31        41        51      | 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  |    211       221       231       241       251         
                                                                                   58-MSE                                                                                                                                           204-MSE                                                    


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with O93646_9EURY | O93646 from UniProtKB/TrEMBL  Length:272

    Alignment length:258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        
         O93646_9EURY     3 RNLVIDITKKPTQNIPPTNEIIEEAITELNVDELLDRLFEKDESGEVITPSRIAKMLEEKAFEIYKEYEKQVREAYLSAGYSREKLEQSFQQARFSRGGKAFEIIFTKLLNKFGIRYEHDRVIKIYDYITEGEKPDFIIPSVRAFLNDPSSAILITVKRKVRERWREAVGEAQILRNKFGDEINFWFVGFDEEFTIYSAIAMLDNGIDRVYVIDGRYDSLIEEIKRISDPNFNEDKYIQKIRRFSDIFDDIIQFLNKH 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh.hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.................eee.hhhhhhhhhhhheeeee......hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhh....eeeehhhhhhhhhhhhhh......hhhhhhhheee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bm3 B   3 RNLVIDITKKPTQNIPPTNEIIEEAITELNVDELLDRLFEKDESGEVITPSRIAKmLEEKAFEIYKEYEKQVREAYLSAGYSREKLEQSFQQARFSRGGKAFEIIFTKLLNKFGIRYEHDRVIKIYDYITEGEKPAFIIPSVRTFLNDPSSAILITVKRKVRERWREAVGEAQILRNKFGDEINFWFVGFDEEFTIYSAIAmLDNGIDRVYVIDGRYDSLIEEIKRISDPNFNEDKYIQKIRRFSDIFDDIIQFLNKH 260
                                    12        22        32        42        52     |  62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 |     212       222       232       242       252        
                                                                                  58-MSE                                                                                                                                           204-MSE                                                    


Chain C from PDB  Type:DNA  Length:11
                                           
                 3bm3 C  -5 CATCCAGGTAC   5
                                     4 


Chain D from PDB  Type:DNA  Length:11
                                           
                 3bm3 D  -6 GGTACCTGGAT   4
                                     3
   Legend:   → Mismatch (orange background)
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  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 3BM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BM3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O93646_9EURY | O93646)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    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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