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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS
 
Authors :  F. K. Winkler, D. W. Banner, C. Oefner, D. Tsernoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos, K. S. Wilson
Date :  19 Mar 91  (Deposition) - 15 Jan 92  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Protein-Dna Complex, Double Helix, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. K. Winkler, D. W. Banner, C. Oefner, D. Tsernoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos, K. S. Wilson
The Crystal Structure Of Ecorv Endonuclease And Of Its Complexes With Cognate And Non-Cognate Dna Fragments.
Embo J. V. 12 1781 1993
PubMed-ID: 8491171
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3')
    Chains: C, D, E, F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTEIN (ECO RV (E.C.3.1.21.4))
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RVE)

(-) Sites  (0, 0)

(no "Site" information available for 2RVE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RVE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 2RVE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RVE)

(-) Exons   (0, 0)

(no "Exon" information available for 2RVE)

(-) 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:213
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
           T2E5_ECOLX     2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWI 240
               SCOP domains d2rvea_ A:      Restriction endonuclease EcoRV                                                                                                                                                                                                  SCOP domains
               CATH domains 2rveA00 A:2     -240  [code=3.40.600.10, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh-----..eeeee.....eee.....hhhhhhhhhhhhhhhhhhhhh...eee..........eeeee..eeeeeeeeeeeeeee.........eeee..hhhhhh......hhh.eeeeeeeeeeee.---------....hhhhhh....eeeeeeeeehhhheeeee..---.eeee...hhhhhhhh.....hhhhhhhhhhh..---------..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rve A   2 SLRSDLINALY-----YDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTR---------TYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGS---TNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYE---------YNNISEYRNWI 240
                                    11|     | 21        31        41        51        61        71        81        91       101       111       121       131        |-       151       161       171       181 |   | 191       201       211        |-       231         
                                     12    18                                                                                                                       140       150                              183 187                              220       230          


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with T2E5_ECOLX | P04390 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:240
                                    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 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIY 241
               SCOP domains d2rveb_ B:        Restriction endonuclease EcoRV                                                                                                                                                                                                 SCOP domains
               CATH domains 2rveB00 B:2       -241  [code=3.40.600.10, no name defined]                                                                                                                                                                                      CATH domains
           Pfam domains (1) ---Endonuc-       EcoRV-2rveB01 B:5-241                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ---Endonuc-       EcoRV-2rveB02 B:5-241                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh-------...eee...eee....hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeee.---------.ee.hhhhhh.......eeeeeehhhhh......---.eee....hhhhhhhh.....hhhhhhhhhhhh.---------..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rve B   2 SLRSDLINALY-------VCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTR---------TYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGS---TNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYE---------YNNISEYRNWIY 241
                                    11|       21        31        41        51        61        71        81        91       101       111       121       131        |-       151       161       171       181 |   | 191       201       211        |-       231       241
                                     12      20                                                                                                                     140       150                              183 187                              220       230           


Chain C from PDB  Type:DNA  Length:8
                                        
                 2rve C   1 CGAGCTCG   8


Chain D from PDB  Type:DNA  Length:8
                                        
                 2rve D   1 CGAGCTCG   8


Chain E from PDB  Type:DNA  Length:8
                                        
                 2rve E   1 CGAGCTCG   8


Chain F from PDB  Type:DNA  Length:8
                                        
                 2rve F   1 CGAGCTCG   8
   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  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Endonuc-EcoRV] (9)

(-) Gene Ontology  (8, 8)

Asymmetric 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: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: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.
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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    Tyr A:72 - Pro A:73   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2E5_ECOLX | P04390: 1az0 1az3 1az4 1b94 1b95 1b96 1b97 1bgb 1bss 1bsu 1bua 1eo3 1eo4 1eon 1eoo 1eop 1rv5 1rva 1rvb 1rvc 1rve 1stx 1suz 1sx5 1sx8 2b0d 2b0e 2ge5 4rve 5f8a 5hlk

(-) Related Entries Specified in the PDB File

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