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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
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEXM
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePOLM, POLMU
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOL MU,TERMINAL TRANSFERASE
 
Molecule 2 - DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
    ChainsT
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*CP*GP*TP*A)-3')
    ChainsP
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - DNA (5'-D(P*GP*CP*CP*G)-3')
    ChainsD
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 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)
  - → 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 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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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLM_HUMAN | Q9NP872dun 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