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(-) Description

Title :  ECORV BOUND TO MN2+ AND COGNATE DNA CONTAINING A 3'S SUBSTITION AT THE CLEAVAGE SITE
 
Authors :  N. C. Horton, B. A. Connolly, J. J. Perona
Date :  21 Mar 00  (Deposition) - 04 Apr 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Restriction Endonuclease, Dna Analog, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. C. Horton, B. A. Connolly, J. J. Perona
Inhibition Of Ecorv Endonuclease By Deoxyribo-3'-S-Phosphorothiolates: A High-Resolution X-Ray Crystallographic Study
J. Am. Chem. Soc. V. 122 3314 2000
PubMed: search  |  Reference-DOI: 10.1021/JA993719J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)- 3')
    ChainsC, D
    EngineeredYES
    SyntheticYES
 
Molecule 2 - TYPE II RESTRICTION ENZYME ECORV
    ChainsA, B
    EC Number3.1.21.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymENDONUCLEASE ECORV, R.ECORV

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2MN5Ligand/IonMANGANESE (II) ION
3TSP2Mod. Nucleotide3'-THIO-THYMIDINE-5'-PHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:45 , ASP A:74 , HOH A:619 , HOH A:678 , HOH A:686 , HOH B:698BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWARELYS A:102 , HIS A:193 , HOH A:624 , HOH A:687 , HOH A:710 , HOH A:719 , GLU B:158BINDING SITE FOR RESIDUE MN A 502
3AC3SOFTWAREHIS A:71 , HOH A:607 , HOH A:689 , HOH A:706BINDING SITE FOR RESIDUE MN A 503
4AC4SOFTWAREGLU A:45 , ASP A:74 , ILE A:91 , HOH A:618 , HOH A:662 , HOH C:23BINDING SITE FOR RESIDUE MN A 504
5AC5SOFTWAREHIS B:71 , HOH B:622 , DT C:11 , HOH C:84 , HOH C:184BINDING SITE FOR RESIDUE MN B 505
6AC6SOFTWAREASN A:15 , TYR A:18 , ASP A:19 , VAL A:20 , PHE A:44 , PHE A:47 , TYR A:163 , HOH A:655BINDING SITE FOR RESIDUE ACY A 601
7AC7SOFTWARETYR B:18 , ASP B:19 , VAL B:20 , PHE B:44BINDING SITE FOR RESIDUE ACY B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EO4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:72 -Pro A:73
2Tyr B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EO4)

(-) Exons   (0, 0)

(no "Exon" information available for 1EO4)

(-) 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:238
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           T2E5_ECOLX     2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
               SCOP domains d1eo4a_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1eo4A00 A:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee...eee....hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee.---hhhhh.ee.--.......eeeeeeeeeehhhhh..........eee....hhhhhhh......hhhhhhhhhhh......-......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eo4 A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRV---KSSLKTYNI--LNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQ-RNDKYNNISEYRNWIYRGRK 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   |   151 |  |  161       171       181       191       201       211       221  | |  231       241    
                                                                                                                                                                     141 145     153  |                                                                 224 |                   
                                                                                                                                                                                    156                                                                   226                   

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           T2E5_ECOLX     2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
               SCOP domains d1eo4b_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1eo4B00 B:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee....eee...hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee..---....eeee..............hhh.eeeeeeeeeeeee.-----.....hhhhhhhh...eeeeeeeeeehhhheeeee......eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eo4 B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNK---KIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRV-----SLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 245
                                    11        21        31        41        51        61        71        81        91      |  -|      111       121       131       141     | 151       161       171       181       191       201       211       221       231       241    
                                                                                                                           98 102                                    141   147                                                                                                  

Chain C from PDB  Type:DNA  Length:10
                                          
                 1eo4 C   2 AAGAtATCTT  11
                                |   11
                                6-TSP 

Chain D from PDB  Type:DNA  Length:10
                                          
                 1eo4 D   1 CAAGAtATCT  10
                                 |  10
                                 6-TSP

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EO4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (T2E5_ECOLX | P04390)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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.
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
        T2E5_ECOLX | P043901az0 1az3 1az4 1b94 1b95 1b96 1b97 1bgb 1bss 1bsu 1bua 1eo3 1eon 1eoo 1eop 1rv5 1rva 1rvb 1rvc 1rve 1stx 1suz 1sx5 1sx8 2b0d 2b0e 2ge5 2rve 4rve 5f8a 5hlk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EO4)