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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (D225A) IN COMPLEX WITH 5' RECESSED-END DNA (RVIII)
 
Authors :  Y. Shi, L. S. Beese
Date :  28 Feb 17  (Deposition) - 24 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
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
    Chains: Z
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-352
    Gene: EXO1, EXOI, HEX1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEXO1, EXONUCLEASE I, HEXOI
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*TP*CP*AP*T)-3')
    Chains: A
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1DA1Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
2MN6Ligand/IonMANGANESE (II) ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC B:1 , ASP Z:152 , ASP Z:171 , ASP Z:173 , HOH Z:533binding site for residue MN Z 401
2AC2SOFTWAREDC B:1 , DA B:102 , ASP Z:152 , HOH Z:512 , HOH Z:513 , HOH Z:521binding site for residue MN Z 402
3AC3SOFTWARECYS Z:80 , ILE Z:325 , HOH Z:577binding site for residue MN Z 403
4AC4SOFTWAREGLU Z:302 , ASP Z:303binding site for residue MN Z 404
5AC5SOFTWAREDA A:5 , HOH A:204 , SER Z:222 , SER Z:229 , ILE Z:233 , HOH Z:524binding site for residue NA Z 405
6AC6SOFTWAREDC A:11 , GLU Z:44binding site for residue MN A 101
7AC7SOFTWAREDG B:7binding site for residue MN B 101
8AC8SOFTWAREDT A:10 , DC B:1 , HOH B:201 , HOH B:203 , HIS Z:36 , ARG Z:92 , ARG Z:96 , MN Z:402 , HOH Z:513 , HOH Z:521 , HOH Z:557binding site for residue DA B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V0A)

(-) Exons   (0, 0)

(no "Exon" information available for 5V0A)

(-) 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    
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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
                                             
                 5v0a A   1 CGCTAGTCGTCAT  13
                                    10   


Chain B from PDB  Type:DNA  Length:9
                                         
                 5v0a B   1 CGACTAGCG   9


Chain Z from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeee.hhhh..eeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh....eee...hhhhhh...eeee......eeeeee.hhhhhhhhhh...hhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhheeee....eeee........hhhhhhhhh...hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v0a Z   2 GIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCAYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTLY 356
                                    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
   Legend:   → Mismatch (orange background)
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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 5V0A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V0A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V0A)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5v0a
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  EXO1_HUMAN | Q9UQ84
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        EXO1_HUMAN | Q9UQ84: 3qe9 3qea 3qeb 5uzv 5v04 5v05 5v06 5v07 5v08 5v09 5v0b 5v0c 5v0d 5v0e

(-) Related Entries Specified in the PDB File

5uzv 5v04 5v05 5v06 5v07 5v08 5v09 5v0b 5v0c 5v0d 5v0e