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(-) Description

Title :  X-RAY STRUCTURE DIHYDROFOLATE REDUCTASE/THYMIDYLATE SYNTHASE FROM BABESIA BOVIS AT 2.35A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Jun 09  (Deposition) - 18 Aug 09  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Babesia Bovis, Dihydrofolate Reductase, Thymidylate Synthase, Methyltransferase, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Begley, T. E. Edwards, A. C. Raymond, E. R. Smith, R. C. Hartley, J. Abendroth, B. Sankaran, D. D. Lorimer, P. J. Myler, B. L. Staker, L. J. Stewart
Inhibitor-Bound Complexes Of Dihydrofolate Reductase-Thymidylate Synthase From Babesia Bovis.
Acta Crystallogr. , Sect. F V. 67 1070 2011
PubMed-ID: 21904052  |  Reference-DOI: 10.1107/S1744309111029009

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE/THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-HISSMT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BBOV_II000780
    Organism Scientific: BABESIA BOVIS
    Organism Taxid: 484906
    Strain: T2BO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:248 , ARG A:413 , ARG B:374BINDING SITE FOR RESIDUE CL A 601
2AC2SOFTWAREARG B:248 , ARG B:413BINDING SITE FOR RESIDUE CL B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I3R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I3R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I3R)

(-) Exons   (0, 0)

(no "Exon" information available for 3I3R)

(-) 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:489
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:506
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504      
         A7ASX7_BABBO     5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMS 510
               SCOP domains d3i3ra1 A:5-187 automated matches                                                                                                                                                              ---------d3i3r  a2 A:205-510 automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eee.........hhhhhhhhhhhhh..hhhhhhhh....eeeeee.....-------....eeeeee..........eee.hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeee.......ee.......eeeeee...ee....eeeeeeeee.--------.hhhhhhh......--...........ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhhhh.eeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3r A   5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYE-------PLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERK--------PPFDQLLMTGTDIS--KPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMS 510
                                    14        24        34        44        54        64      |  -    |   84        94       104       114       124       134       144       154       164       174       184  |      - |     204    |  214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504      
                                                                                             71      79                                                                                                         187      196          209  |                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                         212                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:477
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:501
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504 
         A7ASX7_BABBO     5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPI 505
               SCOP domains d3i3rb1 B:5-187 automated matches                                                                                                                                                              ---------d3i3r  b2 B:205-505 automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eee.........hhhhhhhhhhhhhh...------.....eeeee.....--------....eeeee..........eee.hhhhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeeeeee.......ee.......eeeeee...ee....eeeeeeeee.--------.hhhhhhh......--...........ee...hhhhhhhhhhhhhhheee.......eeeeeeeeeeee..............hhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3r B   5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPP------PDIQNVVIFGRKTYE--------LKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERK--------PPFDQLLMTGTDIS--KPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPI 505
                                    14        24        34        44     |   -  |     64      |  -     |  84        94       104       114       124       134       144       154       164       174       184  |      - |     204    |  214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504 
                                                                        50     57            71       80                                                                                                        187      196          209  |                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                         212
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I3R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I3R)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A7ASX7_BABBO | A7ASX7)
molecular function
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004799    thymidylate synthase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
    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:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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 Related Entries

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

UniProtKB/TrEMBL
        A7ASX7_BABBO | A7ASX7: 3k2h 3kjr 3nrr

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