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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-1) 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 :  1.53
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*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'
    Chains: B
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*AP*CP*GP*T*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, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2SO44Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:264 , GLU A:469 , GLN A:470 , ASP A:471 , ARG A:472 , LEU A:473 , LEU A:767 , HIS A:768 , HOH A:886 , HOH A:1194 , HOH A:1259BINDING SITE FOR RESIDUE DCP A 201
2AC2SOFTWAREHOH A:11 , HOH A:57 , HOH A:79 , HOH A:135 , HOH A:177 , HOH A:180 , GLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , LEU A:395 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:994 , HOH A:1009 , HOH A:1081 , HOH A:1134BINDING SITE FOR RESIDUE SUC A 901
3AC3SOFTWAREHOH A:7 , HIS A:682 , ARG A:702 , LYS A:706 , HOH A:1065BINDING SITE FOR RESIDUE SO4 A 1
4AC4SOFTWAREHOH A:91 , LYS A:298 , MET A:299 , ALA A:300 , ARG A:343 , ARG A:677 , HOH A:941BINDING SITE FOR RESIDUE SO4 A 2
5AC5SOFTWAREHOH A:227 , HIS A:568 , ARG A:779 , ARG A:819 , HOH A:1415BINDING SITE FOR RESIDUE SO4 A 3
6AC6SOFTWARESER A:645 , ARG A:729 , HOH A:1068 , HOH A:1180BINDING SITE FOR RESIDUE SO4 A 4

(-) SS Bonds  (0, 0)

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

(-) 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 3TAN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TAN)

(-) 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 d3tana1 A:297-468 automated matches                                                                                                                                         d3tana2 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.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh................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
                 3tan 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:10
                                          
                 3tan B  20 GCGATCACGC  29
                                    29


Chain C from PDB  Type:DNA  Length:11
                                           
                 3tan C   4 ACGTGATCGCA  14
                                    13
   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 3TAN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu A:620 - Pro A:621   [ RasMol ]  
 

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  3tan
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  2.7.7.7
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3tap CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-3) POSITION
3taq CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-4) 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