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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE ECORII MUTANT R88A
 
Authors :  X. E. Zhou, Y. Wang, M. Reuter, M. Mucke, D. H. Kruger, E. J. Meehan, L. Chen
Date :  26 Nov 02  (Deposition) - 16 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Site-Specific Restriction; Mutation; Replication, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. E. Zhou, Y. Wang, M. Reuter, M. Mucke, D. H. Kruger, E. J. Meehan, L. Chen
Crystal Structure Of Type Iie Restriction Endonuclease Ecorii Reveals An Autoinhibition Mechanism By A Novel Effector-Binding Fold.
J. Mol. Biol. V. 335 307 2004
PubMed-ID: 14659759  |  Reference-DOI: 10.1016/J.JMB.2003.10.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE ECORII
    Chains: A, B
    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
    Gene: ECORII
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ECORII;
TYPE II RESTRICTION ENZYME ECORII

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NA6)

(-) Sites  (0, 0)

(no "Site" information available for 1NA6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NA6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:302 -Pro A:303
2Phe B:302 -Pro B:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NA6)

(-) Exons   (0, 0)

(no "Exon" information available for 1NA6)

(-) 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:365
 aligned with T2E2_ECOLX | P14633 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:395
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
           T2E2_ECOLX     4 SVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSRHFGKTRNEKRITRWVEAAHFRILKITGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGLSLQQAPVNHKYILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTG 398
               SCOP domains d1na6a1 A:4-178 Restriction en   donuclease EcoRII, N-terminal domain                                                                                                          d1na6a2 A:179-398 Restriction      endonuclease EcoRII, C-terminal domain                                                                                                                                                    SCOP domains
               CATH domains 1na6A01 A:4-177 At1g16640 B3 d   omain                                                                                                                                        ------------------------------     ------------------------------------------------------------------------------       ------------    -   -------------------        ------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.eeeeeee.hhhhhh..---......hhhhhhhhhhhhh.......eeeeeeee.......eeeeeeeehhhhh.....eeeee.....hhhhhhhhh..eeeeeee.........eeeeee..hhhhhhhhhhhhh.......eeeehhhhh................hhhhhh...hhhhhhhhhhhh.-----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..........-------......hhhhhh----.---....eee......hhhhhh--------.eee.....hhhhhhhhhh....ee.hhhhhh.....hhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1na6 A   4 SVFHNWLLEIACENYFVYIKRLSANDTGAT---QVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGLSLQQAPVNHKYILPEDWHLRFPSGSEIIQYAASHY-----DPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQA-------PDFLFPSAGAYH----P---LRMLAVKTTCKDRWRQILN--------HLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTG 398
                                    13        23        33   |    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   |   213       223       233       243       253       263       273       283      |  -    |  303     |   -|   |  323       333  |      - |     353       363       373       383       393     
                                                        33  37                                                                                                                                                                       207   213                                                                          290     298        309  314 318               336      345                                                     


Chain B from PDB  Type:PROTEIN  Length:395
 aligned with T2E2_ECOLX | P14633 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:399
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393         
           T2E2_ECOLX     4 SVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSRHFGKTRNEKRITRWVEAAHFRILKITGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGLSLQQAPVNHKYILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYAD 402
               SCOP domains d1na6b1 B:4-178 Restriction endonuclease EcoRII, N-terminal domain                                                                                                             ----d1na6b2 B:183-402 Restriction endonuclease EcoRII, C-terminal domain                                                                                                                                                         SCOP domains
               CATH domains 1na6B01 B:4-177 At1g16640 B3 domain                                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------EcoRII-N-1na6B01 B:12-168                                                                                                                                    ------------------------------------------------------------EcoRII-C-1na6B03 B:229-393                                                                                                                                           --------- Pfam domains (1)
           Pfam domains (2) --------EcoRII-N-1na6B02 B:12-168                                                                                                                                    ------------------------------------------------------------EcoRII-C-1na6B04 B:229-393                                                                                                                                           --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh..eeeeeee...............eeehhhhhhhhhhhhh.......eeeeeeee.......eeeeeeeehhhhh.....eeeee.....hhhhhhhhh..eeeeeee.........eeeeee..hhhhhhhhhhhhh.......eeeehhhhhh........----...hhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................ee.hhhhhhh...hhhhheeeee.......hhhhh........eeee......hhhhhhhhhhh.eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1na6 B   4 SVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSAHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGLSLQQAP----YILPEDWHLRFPSGSEIIQYAASHYVKNSLDPDEQLLDRRRVEYDIFLLVEELHVLDIIRKGFGSVDEFIALANSVSNRRKSRAGKSLELHLEHLFIEHGLRHFATQAITEGNKKPDFLFPSAGAYHDTEFPVENLRMLAVKTTCKDRWRQILNEADKIHQVHLFTLQEGVSLAQYREMRESGVRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYAD 402
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    |  183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393         
                                                                                                                                                                                                        178  183
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DNA_b-psBarrel (3)
(-)
Clan: PDDEXK (13)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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

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        T2E2_ECOLX | P14633: 3hqg

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