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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH THE ARTIFICIAL BASE PAIR DDS-DPXTP
 
Authors :  K. Betz, A. Marx, K. Diederichs, I. Hirao, M. Kimoto
Date :  31 Mar 17  (Deposition) - 28 Jun 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase, Artificial Base Pair, Unnatural Base Pair, Ternary Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Betz, M. Kimoto, K. Diederichs, I. Hirao, A. Marx
Structural Basis For Expansion Of The Genetic Alphabet With An Artificial Nucleobase Pair.
Angew. Chem. Int. Ed. Engl. 2017
PubMed-ID: 28594080  |  Reference-DOI: 10.1002/ANIE.201704190

(-) Compounds

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POLA, POL1
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: TAQ POLYMERASE 1
 
Molecule 2 - DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*AP*(DNU) P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 9)

Asymmetric/Biological Unit (7, 9)
No.NameCountTypeFull Name
191N1Mod. Nucleotide[(2~{R},3~{S},5~{R})-3-OXIDANYL-5-(7-THIOPHEN-2-YLIMIDAZO[4,5-B]PYRIDIN-3-YL)OXOLAN-2-YL]METHYLDIHYDROGEN PHOSPHATE
291R1Ligand/Ion[[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-BIS(OXIDANYL)PENT-1-YNYL]-2-NITRO-PYRROL-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGENPHOSPHATE
391T1Ligand/Ion[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-BIS(OXIDANYL)PENT-1-YNYL]-2-NITRO-PYRROL-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGENPHOSPHATE
4ACT1Ligand/IonACETATE ION
5DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
6GOL2Ligand/IonGLYCEROL
7MG2Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:610 , ASP A:785 , MG A:902 , 91T A:904 , 91R A:905 , HOH A:1006 , HOH A:1168binding site for residue MG A 901
2AC2SOFTWAREASP A:610 , TYR A:611 , ASP A:785 , MG A:901 , 91T A:904 , 91R A:905binding site for residue MG A 902
3AC3SOFTWAREPHE A:724 , HOH A:1043binding site for residue ACT A 903
4AC4SOFTWAREARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , ARG A:660 , LYS A:663 , PHE A:667 , TYR A:671 , ASP A:785 , MG A:901 , MG A:902 , 91R A:905 , HOH A:1007 , HOH A:1025 , HOH A:1054 , HOH A:1056 , HOH A:1168 , DOC B:112 , HOH B:208 , 91N C:204 , DG C:205binding site for residue 91T A 904
5AC5SOFTWAREARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , ARG A:660 , LYS A:663 , PHE A:667 , TYR A:671 , ASP A:785 , MG A:901 , MG A:902 , 91T A:904 , HOH A:1007 , HOH A:1025 , HOH A:1054 , HOH A:1056 , HOH A:1168 , DOC B:112 , HOH B:208 , 91N C:204 , DG C:205binding site for residue 91R A 905
6AC6SOFTWAREDC B:111 , HOH B:206 , DG C:205 , DG C:206 , GOL C:302binding site for residue GOL C 301
7AC7SOFTWAREDG C:205 , DG C:206 , GOL C:301 , HOH C:406 , HOH C:409binding site for residue GOL C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:299 -Pro A:300
2Asp A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NKL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NKL)

(-) 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:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeee.........eeeeeeee..eeee..hhhhhhh........hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5nkl A 293 ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832


Chain B from PDB  Type:DNA  Length:12
                                            
                 5nkl B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC


Chain C from PDB  Type:DNA  Length:16
                                                
                 5nkl C 201 AAAxGGCGCCGTGGTC 216
                               |   210      
                               |            
                             204-91N
   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 5NKL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:578 - Pro A:579   [ RasMol ]  
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        DPO1_THEAQ | P19821: 1bgx 1jxe 1ktq 1qss 1qsy 1qtm 1taq 1tau 2ktq 3ktq 3lwl 3lwm 3m8r 3m8s 3ojs 3oju 3po4 3po5 3py8 3rr7 3rr8 3rrg 3rrh 3rtv 3sv3 3sv4 3syz 3sz2 3t3f 4bwj 4bwm 4c8k 4c8l 4c8m 4c8n 4c8o 4cch 4df4 4df8 4dfj 4dfk 4dfm 4dfp 4dle 4dlg 4elt 4elu 4elv 4ktq 4n56 4n5s 4xiu 5e41 5ktq 5szt

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