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(-) Description

Title :  BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH DNA
 
Authors :  A. F. Moon, J. M. Pryor, D. A. Ramsden, T. A. Kunkel, K. Bebenek, L. C. Pede
Date :  31 Jul 13  (Deposition) - 05 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Polymerase, Dna Break Repair, 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
Sustained Active Site Rigidity During Synthesis By Human Dn Polymerase Mu.
Nat. Struct. Mol. Biol. V. 21 253 2014
PubMed-ID: 24487959  |  Reference-DOI: 10.1038/NSMB.2766

(-) 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: POLYMERASE MU LOOP2 DELETION VARIANT, UNP RESIDUES 132-494
    Gene: POLM, POLMU
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL MU, TERMINAL TRANSFERASE
 
Molecule 2 - TEMPLATE STRAND
    Chains: T
    Engineered: YES
    Other Details: SYNETHESIZED BY OLIGOS ETC
    Synthetic: YES
 
Molecule 3 - UPSTREAM PRIMER STRAND
    Chains: P
    Engineered: YES
    Other Details: SYNTHESIZED BY OLIGOS ETC
    Synthetic: YES
 
Molecule 4 - DOWNSTREAM PRIMER STRAND
    Chains: D
    Engineered: YES
    Other Details: SYNTHESIZED BY OLIGOS ETC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:387 , GLY A:433 , ARG A:445 , SER A:458 , CL A:505 , DA P:4 , DT T:6BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWARESER A:172 , GLY A:174 , ARG A:175BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWARETHR A:241 , ILE A:243 , VAL A:246 , HOH A:900 , HOH A:901 , DT P:3 , HOH P:103BINDING SITE FOR RESIDUE NA A 503
4AC4SOFTWAREPHE A:205 , HOH A:778 , HOH A:852 , HOH D:104 , HOH D:106BINDING SITE FOR RESIDUE NA A 504
5AC5SOFTWAREARG A:387 , SER A:458 , GOL A:501 , DA T:7BINDING SITE FOR RESIDUE CL A 505

(-) SS Bonds  (0, 0)

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

(-) 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 4LZG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LZG)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               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.ee....eee....ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lzg A 138 MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA 494
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      |387       397|      419       429       439       449       459       469       479       489     
                                                                                                                                                                                                                                                            364|         397|                                                                                    
                                                                                                                                                                                                                                                             385          410                                                                                    


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


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


Chain T from PDB  Type:DNA  Length:9
                                         
                 4lzg 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 4LZG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  4lzg
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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 4m04 4m0a 4ycx 4yd1 4yd2 5twp 5twq 5twr 5tws 5vz7 5vz8 5vz9 5vza 5vzb 5vzc 5vzd 5vze 5vzf 5vzg 5vzh 5vzi

(-) Related Entries Specified in the PDB File

2ihm 4lzd 4m04 4m0a