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(-) Description

Title :  SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING MODIFIED PYRIMIDINES
 
Authors :  A. Marx, K. Diederichs, S. Obeid
Date :  11 Apr 12  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase, Modified Nucleotides, A Family, Dna Synthesis, Rigid Linker, Elongation Of Modified Dna, Non-Natural Nucleotide, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Obeid, H. Bu Kamp, W. Welte, K. Diederichs, A. Marx
Snapshot Of The Large Fragment Of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 293-832
    GenePOLA, POL1
    Organism ScientificTHERMUS AQUATICUS
    Organism Taxid271
    SynonymTAQ POLYMERASE 1
 
Molecule 2 - DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    Other DetailsDNA PRIMER
    Other Details - SourceDNA SYNTHESIZER
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3')
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    Other DetailsDNA TEMPLATE
    Other Details - SourceDNA SYNTHESIZER
    SyntheticYES

 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
10R71Ligand/Ion[[(2S,5R)-5-[4-AZANYL-5-[2-(4-ETHYNYLPHENYL)ETHYNYL]-2-OXIDANYLIDENE-PYRIMIDIN-1-YL]OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
20R81Mod. Nucleotide[(2S,5R)-5-{4-AMINO-5-[(4-ETHYNYLPHENYL)ETHYNYL]-2-OXOPYRIMIDIN-1(2H)-YL}TETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN PHOSPHATE
3CA1Ligand/IonCALCIUM ION
4EDO2Ligand/Ion1,2-ETHANEDIOL
5GOL4Ligand/IonGLYCEROL
6MG3Ligand/IonMAGNESIUM ION
7PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:610 , GLU A:786 , 0R7 A:902 , HOH A:1019 , HOH A:1048 , HOH A:1129 , HOH A:1196BINDING SITE FOR RESIDUE MG A 901
02AC2SOFTWAREARG 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 , ASP A:785 , MG A:901 , CA A:908 , HOH A:1045 , HOH A:1080 , HOH A:1196 , HOH A:1200 , HOH A:1207 , HOH A:1231 , 0R8 B:112 , DG C:204 , DG C:205BINDING SITE FOR RESIDUE 0R7 A 902
03AC3SOFTWARETHR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , HOH A:1090 , HOH A:1155 , DC C:209 , DC C:210 , HOH C:405BINDING SITE FOR RESIDUE GOL A 903
04AC4SOFTWAREASP A:371 , TRP A:417 , ARG A:431 , ARG A:435BINDING SITE FOR RESIDUE PGE A 904
05AC5SOFTWAREARG A:425 , LEU A:723 , PHE A:724 , GLU A:774 , TYR A:811 , HOH A:1160 , HOH A:1239BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWAREASP A:452 , TYR A:455 , ARG A:593 , ARG A:596 , ILE A:599 , HOH A:1110BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWARELEU A:311 , GLU A:400 , ARG A:405BINDING SITE FOR RESIDUE EDO A 907
08AC8SOFTWAREASP A:610 , TYR A:611 , ASP A:785 , 0R7 A:902BINDING SITE FOR RESIDUE CA A 908
09AC9SOFTWAREHOH B:335 , HOH B:336 , HOH B:337 , HOH B:338 , HOH C:437 , HOH C:444BINDING SITE FOR RESIDUE MG B 201
10BC1SOFTWAREDG C:205 , DG C:206 , HOH C:404 , HOH C:426 , HOH C:429BINDING SITE FOR RESIDUE GOL C 301
11BC2SOFTWAREDG C:214 , HOH C:439 , HOH C:440 , HOH C:441 , HOH C:442 , HOH C:443BINDING SITE FOR RESIDUE MG C 302
12BC3SOFTWAREALA A:570 , ARG A:728 , DG C:206 , DC C:207BINDING SITE FOR RESIDUE EDO C 303

(-) SS Bonds  (0, 0)

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

(-) 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 4ELV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ELV)

(-) 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:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               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......hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4elv A 294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         

Chain B from PDB  Type:DNA  Length:12
                                            
                 4elv B 101 GACCACGGCGCc 112
                                   110 |
                                     112-0R8

Chain C from PDB  Type:DNA  Length:13
                                             
                 4elv C 204 GGGCGCCGTGGTC 216
                                   213   

   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 4ELV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
    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 | P198211bgx 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 4ktq 4n56 4n5s 4xiu 5e41 5ktq 5nkl 5szt

(-) Related Entries Specified in the PDB File

3ojs 3oju 4elt 4elu