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(-) Description

Title :  CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS Y714S MUTANT BOUND TO G:T MISMATCH
 
Authors :  E. Y. Wu, L. S. Beese
Date :  04 Jun 09  (Deposition) - 23 Jun 10  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dna Polymerase I, Dna Replication, Dna-Binding, Dna-Directed Dna Polymerase, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Y. Wu, L. S. Beese
The Structure Of A High Fidelity Dna Polymerase Bound To A Mismatched Nucleotide Reveals An "Ajar" Intermediate Conformation In The Nucleotide Selection Mechanism.
J. Biol. Chem. V. 286 19758 2011
PubMed-ID: 21454515  |  Reference-DOI: 10.1074/JBC.M110.191130

(-) Compounds

Molecule 1 - DNA POLYMERASE I, LARGE FRAGMENT
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 297-876
    Gene: DPO1
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(P*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC OLIGONUCLEOTIDE TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
5SUC1Ligand/IonSUCROSE
6TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:18 , HOH A:71 , HOH A:83 , HOH A:127 , HOH A:157 , MG A:200 , HOH A:204 , HOH A:224 , GLN A:656 , GLU A:658 , HIS A:682 , ARG A:702 , LYS A:706 , PHE A:710 , ASP A:830 , HOH A:889 , HOH A:894 , HOH A:1088 , HOH A:1120 , DOC B:29 , DG C:3 , DG C:4BINDING SITE FOR RESIDUE TTP A 201
2AC2SOFTWAREHOH A:83 , HOH A:157 , TTP A:201 , HOH A:894BINDING SITE FOR RESIDUE MG A 200
3AC3SOFTWAREHOH A:40 , HOH A:48 , HOH A:195 , HOH A:198 , 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:883 , HOH A:924 , HOH A:957 , HOH A:979 , HOH A:1006BINDING SITE FOR RESIDUE SUC A 901
4AC4SOFTWAREHOH A:277 , MET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A 912

(-) SS Bonds  (0, 0)

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

(-) 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 3HPO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HPO)

(-) 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpo A 297 AKMAFTLADRVTEEMLADKAALVVEVVEENYHAAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELcGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVSGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 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
                                                                                                                     388-CME                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:DNA  Length:9
                                         
                 3hpo B  21 CGATCACGc  29
                                    |
                                   29-DOC


Chain C from PDB  Type:DNA  Length:10
                                          
                 3hpo C   3 GGCGTGATCG  12
                                    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  (0, 0)

(no "SCOP Domain" information available for 3HPO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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

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(-) Related Entries Specified in the PDB File

3hp6 CRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I F710Y MUTANT IN AJAR CONFORMATION BOUND TO G:T MISMATCH
3ht3 CRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I V713P MUTANT BOUND TO G:DCTP