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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY ECORV-DNA-LU COMPLEX WITH UNCLEAVED DNA SUBSTRATE. LANTHANIDE BINDING TO ECORV-DNA COMPLEX INHIBITS CLEAVAGE.
 
Authors :  S. S. Sangani, A. D. Kehr, K. Sinha, G. S. Rule, L. Jen-Jacobson
Date :  09 Dec 15  (Deposition) - 09 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Protein-Dna Complex, Lutetium, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Sinha, S. S. Sangani, A. D. Kehr, G. S. Rule, L. Jen-Jacobson
Metal Ion Binding At The Catalytic Site Induces Widely Distributed Changes In A Sequence Specific Protein-Dna Complex.
Biochemistry V. 55 6115 2016
PubMed-ID: 27786446  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00919

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*T)-3')
    ChainsC, D
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 2 - TYPE-2 RESTRICTION ENZYME ECORV
    ChainsA, B
    EC Number3.1.21.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneECORVR
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymR.ECORV,ENDONUCLEASE ECORV,TYPE II RESTRICTION ENZYME ECORV

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2LU2Ligand/IonLUTETIUM (III) ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:45 , ASP A:74 , HOH A:409 , HOH A:422 , HOH A:441 , HOH A:484 , HOH A:523binding site for residue LU A 301
2AC2SOFTWAREASN A:15 , TYR A:18 , ASP A:19 , EDO A:303binding site for residue NA A 302
3AC3SOFTWAREASN A:15 , TYR A:18 , ASP A:19 , VAL A:20 , PHE A:44 , PHE A:47 , NA A:302binding site for residue EDO A 303
4AC4SOFTWAREGLU B:45 , ASP B:74 , HOH B:410 , HOH B:459 , HOH B:464 , HOH B:488binding site for residue LU B 301
5AC5SOFTWAREASN B:15 , TYR B:18 , ASP B:19 , EDO B:303binding site for residue NA B 302
6AC6SOFTWAREASN B:15 , TYR B:18 , ASP B:19 , VAL B:20 , NA B:302binding site for residue EDO B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F8A)

(-) 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 5F8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F8A)

(-) Exons   (0, 0)

(no "Exon" information available for 5F8A)

(-) 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
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeee....eee...hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeeee..eeeeeeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee...hhhhhh..hhhhhhhh...eeeeeeeeeehhhhh..........eee....hhhhhhhh.....hhhhhhhhhhh...hhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f8a A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeee....eee...hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee...hhhhhh..hhhhhhhh...eeeeeeeeeehhhhh..........eee....hhhhhhhh.....hhhhhhhhhhh...hhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f8a B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK 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:12
                                            
                 5f8a C   1 AAAGATATCTTT  12
                                    10  

Chain D from PDB  Type:DNA  Length:12
                                            
                 5f8a D   1 AAAGATATCTTT  12
                                    10  

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  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  (0, 0)

(no "SCOP Domain" information available for 5F8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F8A)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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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 | P043901az0 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 2rve 4rve 5hlk

(-) Related Entries Specified in the PDB File

4orj 4ORJ IS THE SAME PROTEIN-DNA COMPLEX WHERE THE DNA IS CLEAVED
5hlk