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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (D225A) IN COMPLEX WITH 5' RECESSED-END DNA (RVII)
 
Authors :  Y. Shi, L. S. Beese
Date :  28 Feb 17  (Deposition) - 24 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,Z
Keywords :  Exonuclease, Endonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Shi, H. W. Hellinga, L. S. Beese
Interplay Of Catalysis, Fidelity, Threading, And Processivity In The Exo- And Endonucleolytic Reactions Of Human Exonuclease I.
Proc. Natl. Acad. Sci. V. 114 6010 2017 U. S. A.
PubMed-ID: 28533382  |  Reference-DOI: 10.1073/PNAS.1704845114

(-) Compounds

Molecule 1 - EXONUCLEASE 1
    ChainsZ
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-352
    GeneEXO1, EXOI, HEX1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEXO1, EXONUCLEASE I, HEXOI
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*TP*CP*AP*T)-3')
    ChainsA
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(P*AP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MN5Ligand/IonMANGANESE (II) ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC B:2 , ASP Z:152 , ASP Z:171 , ASP Z:173 , HOH Z:510binding site for residue MN Z 401
2AC2SOFTWARECYS Z:80 , HOH Z:578binding site for residue MN Z 402
3AC3SOFTWAREDA A:5 , HOH A:205 , SER Z:222 , SER Z:229 , ILE Z:233 , GLY Z:234 , HOH Z:545binding site for residue NA Z 403
4AC4SOFTWAREDC A:11binding site for residue MN A 101
5AC5SOFTWAREDA B:1 , DC B:2 , ASP Z:152 , HOH Z:513 , HOH Z:519 , HOH Z:532binding site for residue MN B 101
6AC6SOFTWAREDA B:1binding site for residue MN B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V09)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn Z:247 -Pro Z:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V09)

(-) Exons   (0, 0)

(no "Exon" information available for 5V09)

(-) 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:DNA  Length:13
                                             
                 5v09 A   1 CGCTAGTCGTCAT  13
                                    10   

Chain B from PDB  Type:DNA  Length:10
                                          
                 5v09 B   1 ACGACTAGCG  10
                                    10

Chain Z from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeee.hhhh..eeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhh....eee...hhhhhhhhhhhh....eee...hhhhhh...eeee......eeeeee.hhhhhhhhhh...hhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhheeee....eeee........hhhhh.......hhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v09 Z   2 GIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCAYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTLYF 357
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   ||  
                                                                                                                                                                                                                                                                                                                                                                                 345|  
                                                                                                                                                                                                                                                                                                                                                                                  355  

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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 5V09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V09)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn Z:247 - Pro Z:248   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        EXO1_HUMAN | Q9UQ843qe9 3qea 3qeb 5uzv 5v04 5v05 5v06 5v07 5v08 5v0a 5v0b 5v0c 5v0d 5v0e

(-) Related Entries Specified in the PDB File

5uzv 5v04 5v05 5v06 5v07 5v08 5v0a 5v0b 5v0c 5v0d 5v0e