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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A DA16 OLIGONUCLEOTIDE
 
Authors :  C. E. Bell
Date :  22 Mar 13  (Deposition) - 08 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
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, Processive, Dna Repair, 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 - DT16 OLIGONUCLEOTIDE
    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 Taxid: 562
    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, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:215 , MET A:218 , ARG A:256 , LYS B:214 , HIS B:215 , MET B:218 , ARG B:256BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:106 , HIS A:302 , LYS A:305 , SO4 A:508BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREARG A:148 , ARG A:203 , ALA A:393BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWARETYR A:207 , THR A:210 , HIS A:211 , ASN A:390BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREPHE A:209 , ARG A:212BINDING SITE FOR RESIDUE SO4 A 505
6AC6SOFTWARELYS A:198 , PHE A:205 , ASP A:206 , PHE A:209BINDING SITE FOR RESIDUE SO4 A 506
7AC7SOFTWAREPHE A:415 , PRO A:416 , GLY A:417BINDING SITE FOR RESIDUE SO4 A 507
8AC8SOFTWAREARG A:106 , ASP A:139 , ARG A:142 , SER A:233 , GLY A:234 , SO4 A:502BINDING SITE FOR RESIDUE SO4 A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JS4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JS4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JS4)

(-) Exons   (0, 0)

(no "Exon" information available for 4JS4)

(-) 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:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhhh...eeeehhhhhhhhhhhh................hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeee....hhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4js4 A   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467        


Chain B from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhh....eeeehhhhhhhhhhhh................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......eeee....hhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.hhh.eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4js4 B   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAEEIV 475
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   ||  364       374       384       394       404       414       424       434       444       454       464       474 
                                                                                                                                                                                                  176|                                                                                                                                                                           354|                                                                                                                    
                                                                                                                                                                                                   180                                                                                                                                                                            359                                                                                                                    


Chain C from PDB  Type:DNA  Length:15
                                               
                 4js4 C   2 AAAAAAAAAAAAAAA  16
                                    11     


Chain D from PDB  Type:DNA  Length:14
                                              
                 4js4 D   3 AAAAAAAAAAAAAA  16
                                    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 4JS4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JS4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JS4)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  EX1_ECOLI | P04995
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  3.1.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        EX1_ECOLI | P04995: 1fxx 2qxf 3c94 3c95 3hl8 3hp9 4hcb 4hcc 4jrp 4jrq 4js5

(-) Related Entries Specified in the PDB File

4jrp CRYSTAL STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A 5CY-DT13 OLIGONUCLEOTIDE
4jrq CRYSTAL STRUCTURE OF E. COLI EXONUCLEASE I IN COMPLEX WITH A 5CY-DA13 OLIGONUCLEOTIDE
4js5