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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE II RESTRCITION ENDONUCLEASE, ECOO109I COMPLEXED WITH COGNATE DNA
 
Authors :  H. Hashimoto, T. Shimizu, T. Imasaki, M. Kato, N. Shichijo, K. Kita, M. Sato
Date :  22 Nov 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,X,Y  (2x)
Biol. Unit 1:  A,B,X,Y  (1x)
Keywords :  Restriction Endonuclease, Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, T. Shimizu, T. Imasaki, M. Kato, N. Shichijo, K. Kita, M. Sato
Crystal Structures Of Type Ii Restriction Endonuclease Ecoo109I And Its Complex With Cognate Dna
J. Biol. Chem. V. 280 5605 2005
PubMed-ID: 15590682  |  Reference-DOI: 10.1074/JBC.M411684200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3'
    Chains: X
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3'
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - ECOO109IR
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HB101
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TYPE II RESTRICTION ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit (2x): ABXY
Biological Unit 1 (1x): ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , LEU A:125 , HOH A:1018 , HOH A:1022 , DG X:6 , HOH X:27BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWAREASP B:110 , LEU B:125 , HOH B:1004 , HOH B:1066 , DG Y:6 , HOH Y:29BINDING SITE FOR RESIDUE NA B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 4)

Asymmetric Unit
No.ModelResidues
11, 2Glu A:99 -Pro A:100
21, 2Glu B:99 -Pro B:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WTE)

(-) 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:272
 aligned with Q9RPJ3_ECOLX | Q9RPJ3 from UniProtKB/TrEMBL  Length:272

    Alignment length:272
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
         Q9RPJ3_ECOLX     1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
               SCOP domains d1wtea_ A: Restriction endonuclease EcoO109IR                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wteA01 A:1-87,A:212-272 type ii restriction endonuclease, domain 1                    1wteA02 A:88-211 type ii restriction endonuclease, domain 2                                                                 1wteA01 A:1-87,A:212-272                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhh....hhhhhhh.eeee.....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.........hhhhhh.................eeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wte A   1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with Q9RPJ3_ECOLX | Q9RPJ3 from UniProtKB/TrEMBL  Length:272

    Alignment length:272
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
         Q9RPJ3_ECOLX     1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
               SCOP domains d1wteb_ B: Restriction endonuclease EcoO109IR                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wteB01 B:1-87,B:213-272 type ii restriction endonuclease, domain 1                    1wteB02 B:88-212 type ii restriction endonuclease, domain 2                                                                  1wteB01 B:1-87,B:213-272                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhh....hhhhhhh.eeee.....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.........hhhhhh.................eeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wte B   1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  


Chain X from PDB  Type:DNA  Length:13
                                             
                 1wte X   1 ACCGGGCCCTGCC  13
                                    10   


Chain Y from PDB  Type:DNA  Length:13
                                             
                 1wte Y   1 GGCAGGGCCCGGT  13
                                    10
   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  (1, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WTE)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1WTE)

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  1wte
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  3.1.21.4
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 Related Entries

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

UniProtKB/TrEMBL
        Q9RPJ3_ECOLX | Q9RPJ3: 1wtd

(-) Related Entries Specified in the PDB File

1wtd TYPE II RESTRCITION ENDONUCLEASE, ECOO109I