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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE ECORII CATALYTIC C-TERMINAL DOMAIN IN COMPLEX WITH COGNATE DNA
 
Authors :  D. Golovenko, E. Manakova, S. Grazulis, G. Tamulaitiene, V. Siksnys
Date :  06 Jun 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Restriction Endonuclease, Ecorii, Nucleotide Flipping, Protein-Dna Complex, Dna Recognition, Endonuclease, Hydrolase, Magnesium, Nuclease, Restriction System, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Golovenko, E. Manakova, G. Tamulaitiene, S. Grazulis, V. Siksnys
Structural Mechanisms For The 5'-Ccwgg Sequence Recognition By The N- And C-Terminal Domains Of Ecorii.
Nucleic Acids Res. V. 37 6613 2009
PubMed-ID: 19729506  |  Reference-DOI: 10.1093/NAR/GKP699
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE-2 RESTRICTION ENZYME ECORII
    Chains: A
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL CATALYTIC DOMAIN (UNP RESIDUES 183-404)
    Gene: ECORII, ECORIIR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: R.ECORII, TYPE II RESTRICTION ENZYME ECORII, ENDONUCLEASE ECORII
 
Molecule 2 - 5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:328 , DG B:1 , DG B:2 , DG C:1 , DG C:2BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:209 -Asn A:210
2Phe A:302 -Pro A:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HQG)

(-) 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:222
 aligned with T2E2_ECOLX | P14633 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:222
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402  
           T2E2_ECOLX   183 YILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYADIP 404
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eee.hhhhhhh...hhhhheeeeee..hhhhhhhhhhhh.....eeeee.....hhhhhhhhhhh.eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hqg A 183 YILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYADIP 404
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402  


Chain B from PDB  Type:DNA  Length:12
                                            
                 3hqg B  -6 TCGACCAGGCTA   5
                                     3  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3hqg C  -5 TAGCCTGGTCGA   6
                                     4
   Legend:   → Mismatch (orange background)
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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 3HQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (T2E2_ECOLX | P14633)
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.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        T2E2_ECOLX | P14633: 1na6

(-) Related Entries Specified in the PDB File

1na6 ECORII-R88A
3hqf