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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-4) POSITION
 
Authors :  W. Wang, L. S. Beese
Date :  04 Aug 11  (Deposition) - 19 Oct 11  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase I, Protein-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, H. W. Hellinga, L. S. Beese
Structural Evidence For The Rare Tautomer Hypothesis Of Spontaneous Mutagenesis.
Proc. Natl. Acad. Sci. Usa V. 108 17644 2011
PubMed-ID: 22006298  |  Reference-DOI: 10.1073/PNAS.1114496108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE I
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BACILLUS FRAGMENT (UNP RESIDUES 285-876)
    Organism Scientific: GEOBACILLUS
    Organism Taxid: 129337
 
Molecule 2 - 5'-D(*GP*C*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*G)-3'
    Chains: B
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
    Chains: C
    Engineered: YES
    Other Details: TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
3SUC2Ligand/IonSUCROSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:653 , TYR A:654 , ASP A:830 , HOH A:1108BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREHOH A:16 , HOH A:70 , HOH A:106 , HOH A:235 , HOH A:274 , GLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:915 , HOH A:926 , HOH A:979BINDING SITE FOR RESIDUE SUC A 901
3AC3SOFTWAREHOH A:30 , HOH A:51 , HOH A:63 , HOH A:155 , PHE A:539 , GLU A:540 , GLN A:543 , TYR A:554 , GLU A:751 , GLN A:755 , LYS A:758 , ARG A:784 , GLU A:788 , HOH A:1114 , HOH A:1214BINDING SITE FOR RESIDUE SUC A 902
4AC4SOFTWARELYS A:298 , MET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A 877
5AC5SOFTWAREHOH A:163 , HIS A:568 , ARG A:779 , ARG A:819 , HOH A:1032 , HOH A:1310BINDING SITE FOR RESIDUE SO4 A 2
6AC6SOFTWAREARG A:702 , LYS A:706 , HOH A:1222BINDING SITE FOR RESIDUE SO4 A 3
7AC7SOFTWAREHOH A:272 , SER A:645 , SER A:728 , ARG A:729 , HOH A:932BINDING SITE FOR RESIDUE SO4 A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TAQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:620 -Pro A:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TAQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TAQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3TAQ)

(-) 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:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d3taqa1 A:297-468 automated matches                                                                                                                                         d3taqa2 A:469-876 automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3taq A 297 AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876


Chain B from PDB  Type:DNA  Length:11
                                           
                 3taq B  19 GATCACGCACG  29
                                    28 


Chain C from PDB  Type:DNA  Length:13
                                             
                 3taq C   3 ACGTACGTGATCG  15
                                    12
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TAQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TAQ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3TAQ)

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    Glu A:620 - Pro A:621   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

3tan CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-1) POSITION
3tap CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-3) POSITION
3tar CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-6) POSITION
3thv CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDATP-DT IN CLOSED CONFORMATION
3ti0 CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDGTP-DC IN CLOSED CONFORMATION