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(-) Description

Title :  POST-CATALYTIC COMPLEX OF HUMAN POLYMERASE MU (W434H) MUTANT WITH INCOMING UTP
 
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 :  1.95
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/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-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  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOA1Ligand/IonGLYCOLIC ACID
4MG2Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION
6UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:330 , ASP A:332 , ASP A:418 , UTP A:506 , GOA A:507binding site for residue MG A 501
2AC2SOFTWAREASP A:330 , ASP A:332 , UTP A:506 , HOH A:656binding site for residue MG A 502
3AC3SOFTWARETHR A:241 , ILE A:243 , VAL A:246 , DT P:3 , U P:5 , HOH P:105binding site for residue NA A 503
4AC4SOFTWARELEU A:484 , GLU A:485 , HOH A:696 , HOH A:776binding site for residue CL A 504
5AC5SOFTWAREARG A:181 , DG T:3 , DC T:4 , HOH T:113binding site for residue CL A 505
6AC6SOFTWAREGLY 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 , MG A:501 , MG A:502 , GOA A:507 , HOH A:604 , HOH A:639 , HOH A:656 , HOH A:710 , HOH A:714 , HOH A:716 , HOH A:749 , DA P:4 , DA T:5binding site for residue UTP A 506
7AC7SOFTWAREHIS A:329 , ASP A:330 , ASP A:332 , ASP A:418 , MG A:501 , UTP A:506 , HOH A:703 , DT P:3 , DA P:4binding site for residue GOA A 507
8AC8SOFTWAREPRO A:190 , SER A:191 , GLN A:198binding site for residue EDO A 508

(-) SS Bonds  (0, 0)

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

(-) 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 5VZH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VZH)

(-) 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
                 5vzh A 138 MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA 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      
                                                                                                                                                                                                                                                            364|          397|                                                                                    
                                                                                                                                                                                                                                                             384           410                                                                                    


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


Chain P from PDB  Type:DNA  Length:5
                                     
                 5vzh P   1 CGTAU   5


Chain T from PDB  Type:DNA  Length:9
                                         
                 5vzh 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 5VZH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  5vzh
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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 5vzi

(-) Related Entries Specified in the PDB File

5twp 5twq 5twr 5tws