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(-) Description

Title :  THE STRUCTURE OF GIY-YIG ENDONUCLEASE R.ECO29KI
 
Authors :  A. N. S. Mak, A. R. Lambert, B. L. Stoddard
Date :  06 May 10  (Deposition) - 08 Sep 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Type Ii Restriction Endonuclease, Giy-Yig Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. N. Mak, A. R. Lambert, B. L. Stoddard
Folding, Dna Recognition, And Function Of Giy-Yig Endonucleases: Crystal Structures Of R. Eco29Ki.
Structure V. 18 1321 2010
PubMed-ID: 20800503  |  Reference-DOI: 10.1016/J.STR.2010.07.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ECO29KIR
    Chains: A
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15HE
    Expression System Strain: BL21(DE3)/PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECO29KIR
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RESTRICTION ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MX1)

(-) Sites  (0, 0)

(no "Site" information available for 3MX1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MX1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:37 -Pro A:38
2Ser A:88 -Arg A:89
3Pro A:182 -Gly A:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MX1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MX1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MX1)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:208
 aligned with Q46944_ECOLX | Q46944 from UniProtKB/TrEMBL  Length:214

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q46944_ECOLX     3 NKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQGAGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNRIREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNHTPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSK 210
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------RE_Eco29kI-3mx1A01 A:40-210                                                                                                                                                 Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhhhhhhh...ee..........eeeeeee...hhhhhhhhhhh........eeeee..................hhhhhhhhhhhhhhhh....hhh.eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mx1 A   3 NKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQGAGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNRIREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVQAALIKIYKPLWNTVVDGFGNHTPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSK 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
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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 3MX1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MX1)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: RE_Eco29kI] (3)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q46944_ECOLX | Q46944)
molecular function
    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.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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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  Cis Peptide Bonds
    Leu A:37 - Pro A:38   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q46944_ECOLX | Q46944: 3mx4 3nic

(-) Related Entries Specified in the PDB File

3mx4