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(-) Description

Title :  CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
 
Authors :  C. Kaul, M. Mueller, M. Wagner, S. Schneider, T. Carell
Date :  15 Nov 10  (Deposition) - 27 Jul 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase-Dna Complex, Synthetic Biology, Metal Basepair, Replication, Salen Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kaul, M. Mueller, M. Wagner, S. Schneider, T. Carell
Reversible Bond Formation Enables The Replication And Amplification Of A Crosslinking Salen Complex As An Orthogonal Base Pair.
Nature Chem. V. 3 794 2011
PubMed-ID: 21941252  |  Reference-DOI: 10.1038/NCHEM.1117

(-) Compounds

Molecule 1 - DNA POLYMERASE I
    Atcc: 12980
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM 22
 
Molecule 2 - 5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3'
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: POLYDESOXYRIBONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3'
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: POLYDESOXYRIBONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SAY2Mod. Nucleotide[(2R,3S,5R)-3-HYDROXY-5-(3-HYDROXY-4-METHANOYL-PHENYL)OXOLAN-2-YL]METHYL DIHYDROGENPHOSPHATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A1877
2AC2SOFTWAREHIS A:682 , ARG A:702 , LYS A:706BINDING SITE FOR RESIDUE SO4 A1878
3AC3SOFTWAREGLU A:321 , VAL A:322 , GLU A:325 , ARG A:375 , ASP A:425 , TYR A:429 , ARG A:435BINDING SITE FOR RESIDUE MES A1879
4AC4SOFTWARELYS A:381 , TRP A:382 , GLY A:384 , PHE A:490 , ASN A:700 , ARG A:703 , HOH A:2112BINDING SITE FOR RESIDUE MRD A1880

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XY6)

(-) 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 2XY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XY6)

(-) Exons   (0, 0)

(no "Exon" information available for 2XY6)

(-) 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:581
 aligned with E1C9K5_GEOSE | E1C9K5 from UniProtKB/TrEMBL  Length:580

    Alignment length:581
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       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 
         E1C9K5_GEOSE     - -AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 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..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy6 A 296 TAKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875 


Chain B from PDB  Type:DNA  Length:10
                                          
                 2xy6 B  20 GACCxTCCCT  29
                                |   29
                               24-SAY 


Chain C from PDB  Type:DNA  Length:10
                                          
                 2xy6 C   4 AGGGAxGGTC  13
                                 |  13
                                 9-SAY
   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 2XY6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XY6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XY6)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E1C9K5_GEOSE | E1C9K5)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

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 Related Entries

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

UniProtKB/TrEMBL
        E1C9K5_GEOSE | E1C9K5: 2xo7 2xy5 2xy7 2y1i 2y1j 4b9l 4b9m 4b9n 4b9s 4b9t 4b9u 4b9v 4dsi 4dsj 4dsk 4dsl 4dwi 4uqg 4yfu

(-) Related Entries Specified in the PDB File

2xo7 CRYSTAL STRUCTURE OF A DA:O- ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2xy5 CRYSTAL STRUCTURE OF AN ARTIFICIAL SALEN- COPPER BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2xy7 CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASE IN THE PRE-INSERTION SITE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS