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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY ECORV-DNA-LU COMPLEX WITH CLEAVED DNA SUBSTRATE.
 
Authors :  S. S. Sangani, A. D. Kehr, K. Sinha, G. S. Rule, L. Jen-Jacobson
Date :  15 Jan 16  (Deposition) - 09 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
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 - TYPE-2 RESTRICTION ENZYME ECORV
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ECORVR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: R.ECORV,ENDONUCLEASE ECORV,TYPE II RESTRICTION ENZYME ECORV
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*GP*AP*TP)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*TP*CP*TP*TP*TP)-3')
    Chains: E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2LU4Ligand/IonLUTETIUM (III) ION
3NA4Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:100 , LYS A:167 , HIS A:195 , TYR A:196 , LYS A:197 , HOH A:402binding site for residue EDO A 301
02AC2SOFTWAREASP A:210 , GLU A:211 , HOH A:468binding site for residue EDO A 302
03AC3SOFTWAREASN A:15 , TYR A:18 , ASP A:19 , VAL A:20 , PHE A:47 , NA A:305binding site for residue EDO A 303
04AC4SOFTWAREGLU A:45 , ASP A:74 , ASP A:90 , ILE A:91 , LYS A:92 , LU A:307 , HOH A:420 , DA E:7binding site for residue EDO A 304
05AC5SOFTWAREASN A:15 , TYR A:18 , ASP A:19 , EDO A:303 , HOH A:494binding site for residue NA A 305
06AC6SOFTWARETHR A:186 , THR A:187 , HOH A:444 , HOH B:497 , DT C:6binding site for residue NA A 306
07AC7SOFTWAREGLU A:45 , ASP A:74 , EDO A:304 , HOH A:413 , HOH A:420 , DA E:7binding site for residue LU A 307
08AC8SOFTWARELYS A:38 , GLU B:45 , ASP B:74 , LU B:306 , LU B:307 , DA F:7binding site for residue LU A 308
09AC9SOFTWAREASN B:15 , TYR B:18 , ASP B:19 , VAL B:20 , PHE B:47 , NA B:304binding site for residue EDO B 301
10AD1SOFTWAREGLY B:184 , THR B:187 , ARG B:221 , HOH B:424 , HOH B:443binding site for residue EDO B 302
11AD2SOFTWAREARG A:242 , LYS A:245 , ASP B:207 , SER B:208 , ASP B:210 , GLU B:211 , HOH B:448binding site for residue EDO B 303
12AD3SOFTWAREASN B:15 , TYR B:18 , ASP B:19 , EDO B:301 , HOH B:481binding site for residue NA B 304
13AD4SOFTWARETHR B:186 , THR B:187 , HOH B:476 , DT D:6 , HOH D:107binding site for residue NA B 305
14AD5SOFTWARELU A:308 , HOH A:449 , GLU B:45 , ASP B:74 , HOH B:413 , DA F:7binding site for residue LU B 306
15AD6SOFTWARELU A:308 , ASP B:74 , ASP B:90 , HOH B:406 , DA F:7binding site for residue LU B 307

(-) SS Bonds  (0, 0)

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

(-) 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 5HLK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HLK)

(-) 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..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee...hhhhhh..hhhhhhhh...eeeeeeeeeehhhheeeeeee....eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlk 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...hhhhhhhhhhhhhhhhhhhhhhhhh.eee..........eeee.......eeeeeeeeeee.........eeee..............hhh.eeeeeeeeeeeee..............hhhhh...eeeeeeeeeehhhheeeeeee....eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlk 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:6
                                      
                 5hlk C   1 AAAGAT   6


Chain D from PDB  Type:DNA  Length:6
                                      
                 5hlk D   1 AAAGAT   6


Chain E from PDB  Type:DNA  Length:5
                                     
                 5hlk E   7 ATCTT  11


Chain F from PDB  Type:DNA  Length:6
                                      
                 5hlk F   7 ATCTTT  12
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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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 2rve 4rve 5f8a

(-) Related Entries Specified in the PDB File

5f8a 5F8A IS THE SAME ECORV-DNA-LU COMPLEX BUT WITH UNCLEAVED DNA.