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(-) Description

Title :  TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 2-NT GAPPED DNA SUBSTRATE AND AN INCOMING NONHYDROLYZABLE DUMPNPP
 
Authors :  A. F. Moon, R. A. Gosavi, T. A. Kunkel, L. C. Pedersen, K. Bebenek
Date :  20 Feb 15  (Deposition) - 05 Aug 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Polymerase, Dna Repair, Nhej, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Moon, R. A. Gosavi, T. A. Kunkel, L. C. Pedersen, K. Bebenek
Creative Template-Dependent Synthesis By Human Polymerase Mu.
Proc. Natl. Acad. Sci. Usa V. 112 E4530 2015
PubMed-ID: 26240373  |  Reference-DOI: 10.1073/PNAS.1505798112

(-) 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*AP*TP*AP*CP*G)-3')
    Chains: T
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*TP*A)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5MG3Ligand/IonMAGNESIUM ION
6NA1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:330 , ASP A:332 , ASP A:418 , MG A:602 , DUP A:607 , HOH A:770 , DA P:4binding site for residue MG A 601
02AC2SOFTWAREASP A:330 , ASP A:332 , MG A:601 , DUP A:607 , HOH A:850binding site for residue MG A 602
03AC3SOFTWAREPRO A:190 , SER A:191 , PRO A:192 , GLN A:198binding site for residue EDO A 603
04AC4SOFTWARETRP A:455 , PHE A:462 , HOH A:706 , HOH A:708 , HOH T:202binding site for residue GOL A 604
05AC5SOFTWAREHOH A:704 , HOH A:717binding site for residue GOL A 605
06AC6SOFTWAREGLY A:433 , ARG A:445 , SER A:458 , DUP A:607 , HOH A:786 , DA P:4binding site for residue EDO A 606
07AC7SOFTWAREGLY 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 , TRP A:434 , GLY A:436 , MG A:601 , MG A:602 , EDO A:606 , HOH A:702 , HOH A:749 , HOH A:770 , HOH A:773 , HOH A:797 , HOH A:814 , HOH A:834 , HOH A:850 , HOH A:904 , HOH A:922 , HOH A:932 , DA P:4 , DA T:5binding site for residue DUP A 607
08AC8SOFTWARESER A:172 , GLY A:174 , ARG A:175binding site for residue CL A 608
09AC9SOFTWARESER A:474 , GLU A:475 , HOH A:926 , HOH A:963binding site for residue CL A 609
10AD1SOFTWARELEU A:326binding site for residue CL A 610
11AD2SOFTWAREPHE A:385 , ARG A:387 , TRP A:434 , HOH A:759binding site for residue CL A 611
12AD3SOFTWARETHR A:241 , ILE A:243 , VAL A:246 , HOH A:838 , HOH A:982 , DT P:3 , HOH P:114binding site for residue NA A 612
13AD4SOFTWAREHOH D:116 , HOH T:207 , HOH T:216 , HOH T:223 , HOH T:247 , HOH T:255binding site for residue MG T 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YD1)

(-) 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 4YD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YD1)

(-) Exons   (0, 0)

(no "Exon" information available for 4YD1)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee.eeeeeee.........hhhhhhhhhhh...eeeeeee........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eeee....ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yd1 A 138 MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA 494
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367 ||    388       410       420       430       440       450       460       470       480       490    
                                                                                                                                                                                                                                                                 369|             397|                                                                                    
                                                                                                                                                                                                                                                                  381              410                                                                                    


Chain D from PDB  Type:DNA  Length:4
                                    
                 4yd1 D   1 GCCG   4


Chain P from PDB  Type:DNA  Length:4
                                    
                 4yd1 P   1 CGTA   4


Chain T from PDB  Type:DNA  Length:10
                                          
                 4yd1 T   1 CGGCAATACG  10
                                    10
   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 4YD1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YD1)

(-) 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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  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 4yd2 5twp 5twq 5twr 5tws 5vz7 5vz8 5vz9 5vza 5vzb 5vzc 5vzd 5vze 5vzf 5vzg 5vzh 5vzi

(-) Related Entries Specified in the PDB File

4ycx 4YCX CONTAINS THE SAME PROTEIN IN BINARY COMPLEX WITH THE SAME DNA SUBSTRATE
4yd1