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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE II RESTRCITION ENDONUCLEASE, ECOO109I DNA-FREE FORM
 
Authors :  H. Hashimoto, T. Shimizu, T. Imasaki, M. Kato, N. Shichijo, K. Kita, M. S
Date :  22 Nov 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Restriction Endonuclease, Dna-Free From, Hydrolase (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

(-) Compounds

Molecule 1 - 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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:213 , HIS A:216 , GLU B:268BINDING SITE FOR RESIDUE GOL B 301
02AC2SOFTWAREALA A:15 , SER B:23 , THR B:26 , MET B:29 , HOH B:317BINDING SITE FOR RESIDUE GOL B 302
03AC3SOFTWAREGLU A:223 , ASP A:258 , ALA B:261 , GLN B:262 , TRP B:263 , HIS B:264BINDING SITE FOR RESIDUE GOL B 303
04AC4SOFTWARELYS A:9 , GLU A:12 , CYS A:13 , ARG A:83BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREHIS A:47 , GLU B:57 , ILE B:60 , ALA B:61 , ILE B:239BINDING SITE FOR RESIDUE GOL B 305
06AC6SOFTWARESER A:23 , THR A:26 , GLU B:12 , ALA B:15 , LEU B:19BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREASP A:69 , HOH A:328 , ILE B:35 , ASN B:36 , ILE B:59 , LYS B:62BINDING SITE FOR RESIDUE GOL B 307
08AC8SOFTWAREALA A:61 , LYS A:62 , MET A:65 , HIS B:47 , ALA B:58 , ALA B:61 , LYS B:62BINDING SITE FOR RESIDUE GOL B 308
09AC9SOFTWAREASN A:36 , ILE A:43 , ILE A:59 , LYS A:62 , MET B:65 , ASP B:69 , HOH B:312BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREARG B:21 , LYS B:24 , HIS B:63 , LEU B:64 , GLY B:67 , HOH B:328BINDING SITE FOR RESIDUE GOL B 310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WTD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WTD)

(-) 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:264
 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 d1wtda_ A: Restriction endonuclease EcoO109IR                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wtdA01 A:1-86,A:212-272 type ii restriction endonuclease, domain 1                   1wtdA0        2 A:87-211 type ii restriction endonuclease, domain 2                                                          1wtdA01 A:1-86,A:212-272                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...--------..........eeee.....eeeeeee......hhhhhhhhhhhhhhhhhh......eeeeee........hhhhhhhhh...............eeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wtd A   1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDK--------FIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
                                    10        20        30        40        50        60        70        80        90 |       -|      110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
                                                                                                                      92      101                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:267
 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 d1wtdb_ B: Restriction endonuclease EcoO109IR                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wtdB01 B:1-86,B:212-272 type ii restriction endonuclease, domain 1                   1wtdB02 B:87-211 type ii restriction endonuclease, domain 2                                                                  1wtdB01 B:1-86,B:212-272                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhh....hhhhh...eeee.....eeee.........hhhhhhhhhhhhhhhhhhhhhhh.eee..........hhhhhh..-----............ee...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wtd B   1 MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRIL-----GANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE 272
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      |  -  |    190       200       210       220       230       240       250       260       270  
                                                                                                                                                                                                          177   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  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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        Q9RPJ3_ECOLX | Q9RPJ3: 1wte

(-) Related Entries Specified in the PDB File

1wte COMPLEXED WITH COGNATE DNA