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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE/THYMIDYLATE SYNTHASE FROM BABESIA BOVIS DETERMINED USING SLIPCHIP BASED MICROFLUIDICS
 
Authors :  L. Li, W. Du, T. E. Edwards, B. L. Staker, I. Phan, R. Stacy, R. F. Ismagilo Accelerated Technologies Center For Gene To 3D Structure (A Seattle Structural Genomics Center For Infectious Disease (
Date :  03 Nov 09  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Microfluidics, Slipchip, Structural Genomics, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D, Seattle Structural Genomics Center For Infectious Disease, Methyltransferase, Transferase, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Li, W. Du, R. F. Ismagilov
Multiparameter Screening On Slipchip Used For Nanoliter Protein Crystallization Combining Free Interface Diffusion And Microbatch Methods.
J. Am. Chem. Soc. V. 132 112 2010
PubMed-ID: 20000709  |  Reference-DOI: 10.1021/JA908558M

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE/THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Organism Scientific: BABESIA BOVIS T2BO
    Organism Taxid: 484906
    Other Details: GENE: BBOV_II000780
    Strain: T2BO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:15 , ALA A:16 , ILE A:23 , GLY A:24 , ASN A:27 , GLN A:28 , ILE A:29 , GLY A:66 , ARG A:67 , LYS A:68 , THR A:69 , LEU A:88 , SER A:89 , ARG A:90 , THR A:91 , GLU A:102 , ASP A:103 , LEU A:104 , LEU A:123 , GLY A:124 , GLY A:125 , SER A:126 , PHE A:127 , LEU A:128 , TYR A:129 , GLU A:131 , THR A:154 , HOH A:700 , HOH A:797 , HOH A:918 , HOH A:1017BINDING SITE FOR RESIDUE NAP A 512
2AC2SOFTWAREVAL B:15 , ALA B:16 , ILE B:23 , GLY B:24 , HIS B:25 , ASN B:27 , GLN B:28 , ILE B:29 , TRP B:31 , GLY B:66 , ARG B:67 , LYS B:68 , THR B:69 , LEU B:88 , SER B:89 , ARG B:90 , THR B:91 , LEU B:123 , GLY B:124 , GLY B:125 , SER B:126 , PHE B:127 , LEU B:128 , TYR B:129 , GLU B:131 , THR B:154 , HOH B:849 , HOH B:856BINDING SITE FOR RESIDUE NAP B 512
3AC3SOFTWAREHIS A:36 , PHE A:172 , SER A:173 , THR A:174 , ASP A:175 , SER A:266 , ARG A:267 , HOH A:861BINDING SITE FOR RESIDUE NHE A 513
4AC4SOFTWARELYS A:214 , TYR A:215 , VAL A:216 , THR A:464 , HOH A:710BINDING SITE FOR RESIDUE GOL A 514
5AC5SOFTWAREGLU A:284 , LEU A:287 , LYS A:302 , THR A:490 , ILE A:491 , HOH A:931 , HOH A:1044BINDING SITE FOR RESIDUE GOL A 515
6AC6SOFTWAREGLU A:285 , ILE A:306 , TRP A:307 , ASN A:310 , MET A:509 , HOH A:864 , HOH A:888 , HOH A:947BINDING SITE FOR RESIDUE GOL A 516
7AC7SOFTWAREVAL B:17 , ALA B:18 , LEU B:19 , LEU B:146 , HOH B:682 , HOH B:720BINDING SITE FOR RESIDUE GOL B 513
8AC8SOFTWAREVAL A:17 , ALA A:18 , LEU A:19 , LEU A:146 , HOH A:778 , HOH A:950BINDING SITE FOR RESIDUE GOL A 517

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:78 -Pro A:79
2Gly A:124 -Gly A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KJR)

(-) 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:498
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:507
                                    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 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
               SCOP domains d3kjra1 A:5-187 automated matches                                                                                                                                                      -----------------d3kjra2 A:205-511 automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhh.....eeeeehhhhhhhhhhhh.....eeeee..........eee.hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeee.......ee.......eeeeee...ee....eeeeeeeee.---------hhhhhhh...................ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kjr A   5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERK---------PFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
                                    14        24        34        44        54        64        74        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       
                                                                                                                                                                                                                187       197                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:495
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:504
                                    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 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMA 508
               SCOP domains d3kjrb1 B:5-187 automated matches                                                                                                                                                      -----------------d3kjrb2 B:205-508 automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----DHFR_1-3kjrB01 B:10-186                                                                                                                                                          -----------------------------------------Thymidylat_synt-3kjrB03 B:228-508                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) -----DHFR_1-3kjrB02 B:10-186                                                                                                                                                          -----------------------------------------Thymidylat_synt-3kjrB04 B:228-508                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ......eeeeeee....eee.........hhhhhhhhhhhh...hhhhhh......eeeeeehhhhhhh.........eeeeee..........eee.hhhhhhhhhhhhh....eee..hhhhhhhhhhhh.eeeeeeeee.......ee.......eeeeee...ee....eeeeeeeee.---------hhhhhhh...................ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kjr B   5 YEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERK---------PFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMA 508
                                    14        24        34        44        54        64        74        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    
                                                                                                                                                                                                                187       197
   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 3KJR)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)
(-)
Family: DHFR_1 (89)
(-)
Babesia bovis (2)
1aDHFR_1-3kjrB01B:10-186
1bDHFR_1-3kjrB02B:10-186
(-)
Clan: no clan defined [family: Thymidylat_synt] (68)

(-) 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: 3i3r 3k2h 3nrr

(-) Related Entries Specified in the PDB File

3i3r APO STRUCTURE, TRICLINIC CRYSTAL FORM
3k2h STRUCTURE BOUND TO DUMP, PEMETREXED AND NADP RELATED ID: BABOA.01191.A RELATED DB: TARGETDB