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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A 5CY-DA13 OLIGONUCLEOTIDE
 
Authors :  C. E. Bell
Date :  21 Mar 13  (Deposition) - 08 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Exonuclease, Dnaq Superfamily, 3'-5' Ssdna Exonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Korada, T. D. Johns, C. E. Smith, N. D. Jones, K. A. Mccabe, C. E. Bel
Crystal Structures Of Escherichia Coli Exonuclease I In Complex With Single-Stranded Dna Provide Insights Into The Mechanism Of Processive Digestion.
Nucleic Acids Res. V. 41 5887 2013
PubMed-ID: 23609540  |  Reference-DOI: 10.1093/NAR/GKT278

(-) Compounds

Molecule 1 - 5CY-DA13
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 2 - EXODEOXYRIBONUCLEASE I
    Chains: A, B
    EC Number: 3.1.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21(AI)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SBCB, CPEA, XONA, B2011, JW1993
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: EXONUCLEASE I, DNA DEOXYRIBOPHOSPHODIESTERASE, DRPASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:235 , HIS A:302BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:148 , ARG A:203BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARETHR A:210 , HIS A:211BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREPHE A:11 , SER A:38 , LYS A:198 , PHE A:205 , ASP A:206 , PHE A:209BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREPHE A:209 , ARG A:212BINDING SITE FOR RESIDUE SO4 A 505
6AC6SOFTWAREHIS A:130BINDING SITE FOR RESIDUE SO4 A 506
7AC7SOFTWAREASP A:139 , ARG A:142 , SER A:233 , GLY A:234 , MET A:235 , DA C:9BINDING SITE FOR RESIDUE SO4 A 507
8AC8SOFTWAREHIS A:215 , MET A:218 , ARG A:256 , HIS B:215 , MET B:218 , ARG B:256BINDING SITE FOR RESIDUE SO4 B 501
9AC9SOFTWAREHIS B:302 , LYS B:305BINDING SITE FOR RESIDUE SO4 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JRQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JRQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JRQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JRQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4JRQ)

(-) 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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeeeee.......hhhhhhhhh.hhhhhhhhheehhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeeehhhhhhhhhhhh................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.hhh.eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jrq A   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEATPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 ||    365       375       385       395       405       415       425       435       445       455       465       475
                                                                                                                                                                                                 175|                                                                                                                                                                          354|                                                                                                                     
                                                                                                                                                                                                  181                                                                                                                                                                           358                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeeee........hhhhhhhhh.hhhhhhhheehhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeee.hhhhhhhhhhh................hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......eeee....hhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.hhh.eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh......hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jrq B   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 ||    366       376       386       396       406       416       426       436       446       456       466         
                                                                                                                                                                                                  176|                                                                                                                                                                         354|                                                                                                                    
                                                                                                                                                                                                   182                                                                                                                                                                          359                                                                                                                    


Chain C from PDB  Type:DNA  Length:13
                                             
                 4jrq C   1 AAAAAAAAAAAAA  13
                                    10   


Chain D from PDB  Type:DNA  Length:13
                                             
                 4jrq D   1 AAAAAAAAAAAAA  13
                                    10
   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 4JRQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JRQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JRQ)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  3.1.11.1
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 Related Entries

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        EX1_ECOLI | P04995: 1fxx 2qxf 3c94 3c95 3hl8 3hp9 4hcb 4hcc 4jrp 4js4 4js5

(-) Related Entries Specified in the PDB File

4jrp CRYSTAL STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A 5CY-DT13 OLIGONUCLEOTIDE
4js4