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(-) Description

Title :  POST-CATALYTIC COMPLEX OF HUMAN POLYMERASE MU (W434H) MUTANT WITH INCOMING DTTP
 
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 :  1.50
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
    Fragment: UNP RESIDUES 134-494
    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*AP*T)-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  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG4Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION
4TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:319 , GLY A:320 , ARG A:323 , HIS A:329 , ASP A:330 , ASP A:332 , TTP A:702 , MG A:703 , HOH A:810 , HOH A:822 , HOH A:859 , HOH A:953 , DT P:5 , MG P:101 , HOH P:207binding site for residue TTP A 701
02AC2SOFTWAREGLY 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 , THR A:435 , GLY A:436 , LYS A:438 , TTP A:701 , MG A:703 , MG A:704 , NA A:706 , HOH A:810 , HOH A:816 , HOH A:826 , HOH A:859 , HOH A:887 , HOH A:985 , HOH A:1016 , DA P:4 , DT P:5 , MG P:101 , HOH P:207 , HOH P:209 , DA T:5binding site for residue TTP A 702
03AC3SOFTWAREASP A:330 , ASP A:332 , TTP A:701 , TTP A:702 , MG A:704 , NA A:706 , HOH A:887 , DT P:5binding site for residue MG A 703
04AC4SOFTWAREASP A:330 , ASP A:332 , ASP A:418 , TTP A:702 , MG A:703 , HOH A:921 , DA P:4 , DT P:5 , HOH P:209binding site for residue MG A 704
05AC5SOFTWARETHR A:241 , ILE A:243 , VAL A:246 , HOH A:1001 , DT P:3 , DT P:5 , HOH P:216binding site for residue NA A 705
06AC6SOFTWAREASP A:330 , ASP A:332 , ASP A:418 , TTP A:702 , MG A:703 , HOH A:921 , DA P:4 , DT P:5 , HOH P:209binding site for residue NA A 706
07AC7SOFTWAREPHE A:462 , HOH A:821 , HOH T:203binding site for residue EDO A 707
08AC8SOFTWARETHR A:288 , PRO A:289 , LEU A:291 , GLN A:396 , LYS A:413 , HOH A:936binding site for residue EDO A 708
09AC9SOFTWAREPRO A:190 , SER A:191 , PRO A:192 , GLN A:198 , HOH A:922binding site for residue EDO A 709
10AD1SOFTWAREARG A:387 , VAL A:420 , VAL A:421 , HIS A:434 , SER A:458 , HIS A:459 , HOH A:815 , HOH A:932binding site for residue EDO A 710
11AD2SOFTWAREHOH T:217 , HOH T:220 , HOH T:224 , HOH T:240binding site for residue MG T 101
12AD3SOFTWAREHIS A:329 , TTP A:701 , TTP A:702 , HOH A:822 , DA P:4 , DT P:5 , HOH P:207 , HOH P:211binding site for residue MG P 101

(-) SS Bonds  (0, 0)

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

(-) 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 5VZI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VZI)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhhh..eee.....eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eeee....ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vzi A 138 MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA 494
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       386       396||     418       428       438       448       458       468       478       488      
                                                                                                                                                                                                                                                             365|         397|                                                                                    
                                                                                                                                                                                                                                                              385          410                                                                                    


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


Chain P from PDB  Type:DNA  Length:5
                                     
                 5vzi P   1 CGTAT   5


Chain T from PDB  Type:DNA  Length:9
                                         
                 5vzi 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 5VZI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  5vzi
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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 5vzg 5vzh

(-) Related Entries Specified in the PDB File

5twp 5twq 5twr 5tws