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(-) Description

Title :  Y-FAMILY DNA POLYMERASE CHIMERA DBH-DPO4(243-245)-DBH
 
Authors :  P. Mukherjee, R. C. Wilson, J. D. Pata
Date :  14 Nov 13  (Deposition) - 22 Jan 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Translesion Synthesis, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Mukherjee, R. C. Wilson, I. Lahiri, J. D. Pata
Three Residues Of The Interdomain Linker Determine The Conformation And Single-Base Deletion Fidelity Of Y-Family Translesion Polymerases.
J. Biol. Chem. V. 289 6323 2014
PubMed-ID: 24415763  |  Reference-DOI: 10.1074/JBC.M113.537860

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBLR(DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDBH, SACI_0554
    MutationYES
    Organism ScientificSULFOLOBUS ACIDOCALDARIUS
    Organism Taxid2285
    SynonymPOL IV
 
Molecule 2 - 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'
    ChainsP
    EngineeredYES
    Other DetailsPRIMER DNA
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP *C)-3'
    ChainsT
    EngineeredYES
    Other DetailsTEMPLATE DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , ASP A:105 , GLU A:106 , CA A:402 , DCP A:403 , HOH A:508 , DG P:13BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP A:7 , PHE A:8 , ASP A:105 , CA A:401 , DCP A:403BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREASP A:7 , PHE A:8 , ASP A:9 , TYR A:10 , PHE A:11 , PHE A:12 , THR A:45 , TYR A:48 , ARG A:51 , ASP A:105 , LYS A:160 , CA A:401 , CA A:402 , HOH A:513 , DG P:13 , DG T:5BINDING SITE FOR RESIDUE DCP A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NLG)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4nlga1 A:1-241 automated matches                                                                                                                                                                                                                d4nlga2 A:242-344 automated matches                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhh......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eee.hhhhhhhhhhhh........hhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhh...eeeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nlg A   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSRKSHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    

Chain P from PDB  Type:DNA  Length:13
                                             
                 4nlg P   1 GGCACTGATCGGG  13
                                    10   

Chain T from PDB  Type:DNA  Length:18
                                                  
                 4nlg T   2 TACGCCCTGATCAGTGCC  19
                                    11        

   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:160 - Pro A:161   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPO4_SULAC | Q4JB803bq0 3bq1 3bq2 4f4w 4f4x 4f4y 4f4z 4f50 4hyk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NLG)