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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM POLYMERASE BETA: TERNARY P/T COMPLEX
 
Authors :  E. Mejia, M. Burak, A. Alonso, V. Larraga, T. A. Kunkel, K. Bebenek, M. Ga
Date :  12 Mar 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mejia, M. Burak, A. Alonso, V. Larraga, T. A. Kunkel, K. Bebenek, M. Garcia-Diaz
Structures Of The Leishmania Infantum Polymerase Beta.
Dna Repair (Amst. ) V. 18 1 2014
PubMed-ID: 24666693  |  Reference-DOI: 10.1016/J.DNAREP.2014.03.001

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LEISHMANIA INFANTUM
    Organism Taxid: 5671
 
Molecule 2 - DNA (5'-D(*CP*AP*GP*TP*A)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ADE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1D3T1Ligand/Ion2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:183 , SER A:184 , ARG A:187 , SER A:192 , GLY A:193 , ASP A:194 , ASP A:196 , THR A:286 , PHE A:287 , GLY A:289 , LYS A:291 , ASN A:294 , MG A:402 , HOH A:596 , HOH A:599 , HOH A:672 , HOH A:675 , HOH A:681 , HOH A:682 , HOH A:688 , HOH A:728 , DA D:5 , DA E:6binding site for residue D3T A 401
2AC2SOFTWAREASP A:194 , ASP A:196 , D3T A:401 , HOH A:596binding site for residue MG A 402
3AC3SOFTWARETHR A:100 , VAL A:102 , PHE A:105 , DT D:4 , HOH D:104 , HOH D:110binding site for residue NA A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P4M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:289 -Ser A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P4M)

(-) Exons   (0, 0)

(no "Exon" information available for 4P4M)

(-) 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:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhh..eeeeehhhhhh...ee..eeeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeee...eeeeee.............eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..hhhhhh.....ee..eehhhhhh......hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p4m A  90 KPKLKAIQELTQVHGFGPRAAAALFDREGIFTVDELLQKADSIPSLTDQQRVGIKYFYDINEKIPMQESVLHENYLREKCMEVLGKDFSILICGSYRRRHPFSGDVDAILSRTLDAPPLSEPVAATGVLGHFVEFLESLKYLEATMAQGPLKYMGMGRLPPRINTKVYKARRVDIRLIETKSVPTAMLTFTGSKNFNVIMRQAAISKGYLLNEYGLFKLGTPEEARGKNAGEELGVPKDELEDKRVEVRSEQDVFDVLGMPYAKPENRDP 376
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  ||   267       277       287       297       307       317     ||336       346       356       366       376
                                                                                                                                                                                            252|                                                           323|                                           
                                                                                                                                                                                             261                                                            333                                           


Chain D from PDB  Type:DNA  Length:5
                                     
                 4p4m D   1 CAGTA   5


Chain E from PDB  Type:DNA  Length:6
                                      
                 4p4m E   6 ATACTG  11
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  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 4P4M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P4M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P4M)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:289 - Ser A:290   [ RasMol ]  
 

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UniProtKB/TrEMBL
        Q9U6N3_LEIIN | Q9U6N3: 4p4o 4p4p

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