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(-) Description

Title :  PRE-CATALYTIC TERNARY COMPLEX OF HUMAN POLYMERASE MU (W434H) MUTANT WITH INCOMING NONHYDROLYZABLE UMPNPP
 
Authors :  A. F. Moon, J. M. Pryor, D. A. Ramsden, T. A. Kunkel, K. Bebenek, L. C. Pede
Date :  27 May 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Family X Dna Polymerase, Nonhomologous End-Joining, Dna Double Strand Break Repair, Ribonucleotide Incorporation, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Moon, J. M. Pryor, D. A. Ramsden, T. A. Kunkel, K. Bebenek, L. C. Pedersen
Structural Accommodation Of Ribonucleotide Incorporation By The Dna Repair Enzyme Polymerase Mu
Nucleic Acids Res. 2017
PubMed: search  |  Reference-DOI: 10.1093/NAR/GKX527

(-) Compounds

Molecule 1 - DNA-DIRECTED DNA/RNA POLYMERASE MU
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEXM
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POLM, POLMU
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL MU,TERMINAL TRANSFERASE
 
Molecule 2 - DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*TP*A)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
12KH1Ligand/Ion5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE
2CL2Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:319 , GLY A:320 , ARG A:323 , LYS A:325 , GLY A:328 , HIS A:329 , ASP A:330 , ASP A:332 , GLY A:433 , HIS A:434 , GLY A:436 , LYS A:438 , MG A:702 , MG A:703 , EDO A:707 , HOH A:807 , HOH A:826 , HOH A:852 , HOH A:871 , HOH A:874 , HOH A:899 , HOH A:905 , HOH A:909 , HOH A:927 , DA P:4 , DA T:5binding site for residue 2KH A 701
2AC2SOFTWAREASP A:330 , ASP A:332 , ASP A:418 , 2KH A:701 , MG A:703 , HOH A:826 , DA P:4binding site for residue MG A 702
3AC3SOFTWAREASP A:330 , ASP A:332 , 2KH A:701 , MG A:702 , HOH A:871binding site for residue MG A 703
4AC4SOFTWARETHR A:241 , ILE A:243 , VAL A:246 , DT P:3 , HOH P:109 , HOH P:113binding site for residue NA A 704
5AC5SOFTWAREASN A:457 , SER A:458 , EDO A:707 , DA T:7binding site for residue CL A 705
6AC6SOFTWAREARG A:387 , HIS A:434 , SER A:458 , HOH A:813 , HOH A:986binding site for residue CL A 706
7AC7SOFTWAREARG A:387 , GLY A:433 , HIS A:434 , ARG A:445 , SER A:458 , 2KH A:701 , CL A:705 , DA P:4 , DT T:6binding site for residue EDO A 707
8AC8SOFTWAREPRO A:190 , SER A:191 , PRO A:192 , GLN A:198binding site for residue EDO A 708

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:436 -Ser A:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VZG)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeeehhhhh...ee..eeeeee........hhhhhhhhhhhhh..eee......eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eeee....ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vzg A 138 MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA 494
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       385       395 ||    417       427       437       447       457       467       477       487       
                                                                                                                                                                                                                                                             365|          397|                                                                                    
                                                                                                                                                                                                                                                              384           410                                                                                    


Chain D from PDB  Type:DNA  Length:4
                                    
                 5vzg D   1 GCCG   4


Chain P from PDB  Type:DNA  Length:4
                                    
                 5vzg P   1 CGTA   4


Chain T from PDB  Type:DNA  Length:9
                                         
                 5vzg T   1 CGGCATACG   9
   Legend:   → Mismatch (orange background)
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    → 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 5VZG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:436 - Ser A:437   [ RasMol ]  
 

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  5vzg
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  DPOLM_HUMAN | Q9NP87
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLM_HUMAN | Q9NP87: 2dun 2htf 4lzd 4lzg 4m04 4m0a 4ycx 4yd1 4yd2 5twp 5twq 5twr 5tws 5vz7 5vz8 5vz9 5vza 5vzb 5vzc 5vzd 5vze 5vzf 5vzh 5vzi

(-) Related Entries Specified in the PDB File

5twp 5twq 5twr 5tws