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(-) Description

Title :  CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS WITH 2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA
 
Authors :  S. Jiang, J. Gan, H. Sun, Z. Huang
Date :  13 Dec 13  (Deposition) - 17 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Jiang, J. Gan, H. Sun, Z. Huang
Crystal Structure Of Fragment Dna Polymerase I From Bacillu Stearothermophilus With 2'-Mese-Arabino-Guanosine Derivatized Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE I
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDPO1
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
 
Molecule 2 - 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    ChainsB, C
    EngineeredYES
    Other Details2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
11TW2Mod. Nucleotide2-AMINO-9-(2-SE-METHYL-5-O-PHOSPHONO-2-SELENO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE
2GOL1Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
4SO46Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:299 , ALA A:300 , ARG A:343 , ARG A:677 , LYS A:684BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREHIS A:682 , ARG A:702 , LYS A:706 , HOH A:1016BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWARETHR A:308 , GLU A:309 , HOH A:1030BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWAREGLU A:364 , LYS A:367 , GLY A:389 , VAL A:390 , SER A:391BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWAREGLU A:515 , TYR A:519 , PHE A:526 , ASN A:527 , ILE A:528 , ASN A:529 , TYR A:577BINDING SITE FOR RESIDUE SO4 A 905
6AC6SOFTWAREGLU A:667 , ASP A:668 , ASP A:669 , GLY A:745 , ARG A:748 , HOH A:1052BINDING SITE FOR RESIDUE SO4 A 906
7AC7SOFTWAREGLU A:321 , PHE A:371 , ASP A:372 , ARG A:375 , ASP A:409 , VAL A:410 , ASP A:425 , LYS A:450 , NA A:909 , HOH A:1062 , HOH A:1079BINDING SITE FOR RESIDUE GOL A 907
8AC8SOFTWARETHR A:308 , GLU A:310BINDING SITE FOR RESIDUE NA A 908
9AC9SOFTWAREPHE A:371 , ASP A:372 , ARG A:375 , GOL A:907 , HOH A:1060 , HOH A:1061BINDING SITE FOR RESIDUE NA A 909

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O0I)

(-) 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 4O0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O0I)

(-) Exons   (0, 0)

(no "Exon" information available for 4O0I)

(-) 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.eeeeee..............eeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o0i A 297 SKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 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
                                           
                 4o0i B   4 xCGAATTCGCG  14
                            |       13 
                            4-1TW      

Chain C from PDB  Type:DNA  Length:11
                                           
                 4o0i C   4 CxCGAATTCGC  14
                             |      13 
                             5-1TW     

   Legend:   → Mismatch (orange background)
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    → 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 4O0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O0I)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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

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 Related Entries

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

UniProtKB/Swiss-Prot
        D9N168_GEOSE | D9N1684dsi 4dsj 4dsk 4dsl 4dwi
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(-) Related Entries Specified in the PDB File

1kw0 2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA