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(-) Description

Title :  STRUCTURE OF THE K38A MUTANT OF ECORV BOUND TO COGNATE DNA AND MN2+
 
Authors :  N. C. Horton, J. J. Perona
Date :  25 Mar 04  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Restriction Enzyme; Ecorv; Dna; X-Ray Crystallography, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. C. Horton, J. J. Perona
Dna Cleavage By Ecorv Endonuclease: Two Metal Ions In Three Metal Ion Binding Sites
Biochemistry V. 43 6841 2004
PubMed-ID: 15170321  |  Reference-DOI: 10.1021/BI0499056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*AP*GP*AP*T)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(P*AP*TP*CP*TP*T)-3'
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TYPE II RESTRICTION ENZYME ECORV
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBSRV
    Expression System Strain: MM294
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECORVR
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: COMPLEXED WITH CLEAVED DNA DUPLEX
    Synonym: ENDONUCLEASE ECORV

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:45 , ASP B:74 , ASP B:90 , ILE B:91 , DA F:7 , HOH F:276BINDING SITE FOR RESIDUE MN B 1002
2AC2SOFTWAREGLU A:45 , ASP A:74 , ASP A:90 , ILE A:91 , MN A:1004 , DA D:7BINDING SITE FOR RESIDUE MN A 1003
3AC3SOFTWAREGLU A:45 , ASP A:74 , MN A:1003 , HOH A:1186 , HOH A:1187 , DA D:7BINDING SITE FOR RESIDUE MN A 1004
4AC4SOFTWAREGLN A:68 , HIS A:71 , HOH A:1103 , HOH A:1133 , DT F:11BINDING SITE FOR RESIDUE MN A 1005
5AC5SOFTWAREHIS B:71 , HOH B:1108 , HOH B:1109 , DT D:11BINDING SITE FOR RESIDUE MN B 1006
6AC6SOFTWARELYS A:102 , HIS A:193BINDING SITE FOR RESIDUE MN A 1007

(-) SS Bonds  (0, 0)

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

(-) 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 1STX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1STX)

(-) 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:244
 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 d1stxa_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1stxA00 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...hhhhhh.....hhhhh...eeeeeeeeeehhhhh..........eee....hhhhhhhh.....hhhhhhhhhhh...hhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1stx A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTAVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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    


Chain B from PDB  Type:PROTEIN  Length:244
 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 d1stxb_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                            SCOP domains
               CATH domains 1stxB00 B:2-245  [code=3.40.600.10, no name defined]                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ---Endonuc-EcoRV-1stxB01 B:5-244                                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ---Endonuc-EcoRV-1stxB02 B:5-244                                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee...eee....hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee...hhhhhh.ee.hhhhhh...eeeeeeeeeehhhheeeeeee....eeee...hhhhhhhh.....hhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1stx B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTAVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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    


Chain C from PDB  Type:DNA  Length:6
                                      
                 1stx C   1 AAAGAT   6


Chain D from PDB  Type:DNA  Length:5
                                     
                 1stx D   7 ATCTT  11


Chain E from PDB  Type:DNA  Length:6
                                      
                 1stx E   1 AAAGAT   6


Chain F from PDB  Type:DNA  Length:5
                                     
                 1stx F   7 ATCTT  11
   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  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) 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: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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 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 1suz 1sx5 1sx8 2b0d 2b0e 2ge5 2rve 4rve 5f8a 5hlk

(-) Related Entries Specified in the PDB File

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