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(-) Description

Title :  A NEW BIO-ISOSTERIC BASE PAIR BASED ON REVERSIBLE BONDING
 
Authors :  M. Tomas-Gamasa, S. Serdjukov, M. Su, M. Mueller, T. Carell
Date :  23 Jun 14  (Deposition) - 03 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase-Dna Complex, Unnatural Base Pair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tomas-Gamasa, S. Serdjukow, M. Su, M. Muller, T. Carell
"Post-It" Type Connected Dna Created With A Reversible Covalent Cross-Link.
Angew. Chem. Int. Ed. Engl. V. 54 796 2015
PubMed-ID: 25446281  |  Reference-DOI: 10.1002/ANIE.201407854

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: POLYMERASE DOMAIN, RESIDUES 2-580
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM 22
    Synonym: DNA POLYMERASE I FRAGMENT
 
Molecule 2 - 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'
    Chains: B
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: LINK TO CHAIN C VIA RESIDUE SAY
    Synonym: POLYDEOXYRIBONUCLEOTIDE B
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3'
    Chains: C
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: LINK TO CHAIN B VIA RESIDUE T0T
    Synonym: POLYDEOXYRIBONUCLEOTIDE C
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1SAY1Mod. Nucleotide[(2R,3S,5R)-3-HYDROXY-5-(3-HYDROXY-4-METHANOYL-PHENYL)OXOLAN-2-YL]METHYL DIHYDROGENPHOSPHATE
2SO44Ligand/IonSULFATE ION
3SUC1Ligand/IonSUCROSE
4T0T1Mod. Nucleotide(1R)-1-{4-[(E)-2-(2-AMINOPHENYL)ETHENYL]PHENYL}-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONATO-D-ERYTHRO-PENTITOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:2015 , HOH A:2029 , HOH A:2041BINDING SITE FOR RESIDUE SUC A 877
2AC2SOFTWAREMET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A 878
3AC3SOFTWAREHIS A:568 , ARG A:779 , ARG A:819BINDING SITE FOR RESIDUE SO4 A 879
4AC4SOFTWAREHIS A:682 , ARG A:702 , LYS A:706 , HOH A:2134BINDING SITE FOR RESIDUE SO4 A 880
5AC5SOFTWAREGLU A:321 , VAL A:322 , ASP A:425 , TYR A:429BINDING SITE FOR RESIDUE SO4 A 881

(-) SS Bonds  (0, 0)

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

(-) 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 4UQG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UQG)

(-) 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:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uqg A 298 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         


Chain B from PDB  Type:DNA  Length:10
                                          
                 4uqg B  20 GACCxTCCCT  29
                                |   29
                               24-T0T 


Chain C from PDB  Type:DNA  Length:10
                                          
                 4uqg 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 4UQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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

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  E1C9K5_GEOSE | E1C9K5
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        E1C9K5_GEOSE | E1C9K5: 2xo7 2xy5 2xy6 2xy7 2y1i 2y1j 4b9l 4b9m 4b9n 4b9s 4b9t 4b9u 4b9v 4dsi 4dsj 4dsk 4dsl 4dwi 4yfu

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