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(-) Description

Title :  TERNARY COMPLEX STRUCTURE OF KLENOW FRAGMENT OF TAQ DNA POLYMERASE I707L MUTANT (CS3C KLENTAQ) WITH DNA AND DDCTP
 
Authors :  E. Y. Wu
Date :  10 Oct 13  (Deposition) - 21 Jan 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Y. Wu, A. R. Walsh, E. C. Materne, E. P. Hiltner, B. Zielinski, B. R. Miller, L. Mawby, E. Modeste, C. A. Parish, W. M. Barnes, M. B. Kermekchiev
A Conservative Isoleucine To Leucine Mutation Causes Major Rearrangements And Cold Sensitivity In Klentaq1 Dna Polymerase.
Biochemistry V. 54 881 2015
PubMed-ID: 25537790  |  Reference-DOI: 10.1021/BI501198F

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'
    Chains: B
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'
    Chains: C
    Engineered: YES
    Other Details: TEMPLATE STRAND
    Synthetic: YES
 
Molecule 3 - DNA POLYMERASE I, THERMOSTABLE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: KLENOW FRAGMENT (UNP RESIDUES 281-832)
    Gene: POLA, POL1
    Mutation: YES
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: TAQ POLYMERASE 1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 13)

Asymmetric/Biological Unit (7, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2DCT1Ligand/Ion2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5GOL1Ligand/IonGLYCEROL
6MG1Ligand/IonMAGNESIUM ION
7MN6Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:1339 , HOH B:328 , HOH B:329 , HOH B:330 , HOH B:331 , HOH B:333BINDING SITE FOR RESIDUE MN B 201
02AC2SOFTWAREASP A:610 , ASP A:785 , MN A:902 , DCT A:907 , HOH A:1014 , DOC B:112 , HOH B:305BINDING SITE FOR RESIDUE MG A 901
03AC3SOFTWAREASP A:610 , TYR A:611 , ASP A:785 , MG A:901 , DCT A:907BINDING SITE FOR RESIDUE MN A 902
04AC4SOFTWAREHOH A:1236 , HOH A:1331 , HOH A:1332 , HOH A:1333 , HOH A:1334 , HOH A:1335BINDING SITE FOR RESIDUE MN A 903
05AC5SOFTWAREHIS A:443 , HOH A:1342 , HOH A:1343 , HOH A:1344 , HOH A:1345BINDING SITE FOR RESIDUE MN A 904
06AC6SOFTWAREGLU A:462 , GLU A:825 , HOH A:1356 , HOH A:1357BINDING SITE FOR RESIDUE MN A 905
07AC7SOFTWAREGLU A:721 , HOH A:1111 , HOH A:1240 , HOH A:1442 , HOH A:1443BINDING SITE FOR RESIDUE MN A 906
08AC8SOFTWAREARG 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 , LYS A:663 , PHE A:667 , ASP A:785 , MG A:901 , MN A:902 , HOH A:1003 , HOH A:1009 , HOH A:1018 , HOH A:1100 , HOH A:1365 , HOH A:1387 , DOC B:112 , HOH B:304 , HOH B:305 , DG C:204 , DG C:205BINDING SITE FOR RESIDUE DCT A 907
09AC9SOFTWAREARG A:563 , ASN A:565 , SER A:577 , HOH A:1088 , HOH A:1133 , HOH A:1268 , HOH A:1336 , DG C:208 , DC C:209 , HOH C:303 , HOH C:306 , HOH C:310 , HOH C:339BINDING SITE FOR RESIDUE EPE A 908
10BC1SOFTWAREASN A:485 , SER A:486 , ARG A:487 , HOH A:1066 , HOH A:1180 , DG C:211 , DT C:212BINDING SITE FOR RESIDUE ACT A 909
11BC2SOFTWARELEU A:311 , ARG A:405 , HOH A:1187 , HOH A:1224 , HOH A:1333 , HOH A:1335BINDING SITE FOR RESIDUE ACT A 910
12BC3SOFTWARELEU A:670 , TYR A:671 , GLY A:672 , ARG A:746 , HOH A:1444BINDING SITE FOR RESIDUE GOL A 911

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N5S)

(-) 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 4N5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N5S)

(-) Exons   (0, 0)

(no "Exon" information available for 4N5S)

(-) 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:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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..................hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n5s A 290 SPKALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWLEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK 831
                                   299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829  


Chain B from PDB  Type:DNA  Length:12
                                            
                 4n5s B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC


Chain C from PDB  Type:DNA  Length:14
                                              
                 4n5s C 203 AGGGCGCCGTGGTC 216
                                   212
   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 4N5S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N5S)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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    Trp A:299 - Pro A:300   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        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 4xiu 5e41 5ktq 5nkl 5szt

(-) Related Entries Specified in the PDB File

4n56 CS3C KLENTAQ-DNA COMPLEX WITH NO NUCLEOTIDE