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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE/THYMIDYLATE SYNTHASE FROM BABESIA BOVIS WITH DUMP, PEMETREXED AND NADP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Sep 09  (Deposition) - 13 Oct 09  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Alimta, Folic Acid Analog, Thya, Folate Antimetabolites, Tic-Borne Parasitic Protozoan, Babesiosis, Malaria-Like Disease, Methyltransferase, Transferase (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
    ChainsA, B
    EC Number2.1.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePBADSMT
    GeneBBOV_II000780
    Organism ScientificBABESIA BOVIS
    Organism Taxid5865

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2LYA4Ligand/Ion2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOICACID
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:248 , LEU A:390 , CYS A:393 , HIS A:394 , GLN A:412 , ARG A:413 , SER A:414 , CYS A:415 , ASP A:416 , ASN A:424 , HIS A:454 , TYR A:456 , LYA A:513 , HOH A:566 , HOH A:730 , ARG B:373 , ARG B:374BINDING SITE FOR RESIDUE UMP A 512
02AC2SOFTWAREALA A:278 , SER A:281 , ILE A:306 , ASN A:310 , LEU A:390 , ASP A:416 , LEU A:419 , GLY A:420 , PHE A:423 , TYR A:456 , MET A:509 , SER A:510 , UMP A:512 , HOH A:559 , HOH A:653 , HOH A:690 , HOH A:694 , HOH A:710 , HOH A:735 , HOH A:794 , HOH A:843BINDING SITE FOR RESIDUE LYA A 513
03AC3SOFTWAREPHE A:14 , VAL A:15 , ALA A:16 , ASP A:37 , PHE A:38 , ARG A:39 , LEU A:41 , ARG A:42 , SER A:77 , ARG A:83 , LEU A:123 , TYR A:129 , THR A:144 , NAP A:515 , HOH A:571 , HOH A:575 , HOH A:608 , HOH A:664BINDING SITE FOR RESIDUE LYA A 514
04AC4SOFTWAREVAL A:15 , ALA A:16 , ILE A:23 , GLY A:24 , HIS A:25 , ASN A:27 , GLN A:28 , ILE A:29 , TRP A:31 , GLY A:66 , ARG A:67 , LYS A:68 , THR A:69 , SER A:72 , 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:125 , SER A:126 , PHE A:127 , TYR A:129 , GLU A:131 , THR A:154 , LYA A:514 , HOH A:587 , HOH A:721 , ARG B:305BINDING SITE FOR RESIDUE NAP A 515
05AC5SOFTWAREGLN A:358 , GLU A:361 , ILE A:376 , HOH A:858 , TRP B:380 , VAL B:382 , LEU B:385BINDING SITE FOR RESIDUE EDO A 516
06AC6SOFTWARETRP A:380 , VAL A:382 , LEU A:385 , ILE B:356 , GLN B:358 , GLU B:361 , ILE B:362 , ILE B:376 , HOH B:622BINDING SITE FOR RESIDUE EDO A 517
07AC7SOFTWAREARG A:374 , ASN B:319 , ALA B:389 , PRO B:391 , HOH B:691BINDING SITE FOR RESIDUE EDO B 517
08AC8SOFTWAREARG A:373 , ARG A:374 , ARG B:248 , LEU B:390 , CYS B:393 , HIS B:394 , GLN B:412 , ARG B:413 , SER B:414 , CYS B:415 , ASP B:416 , ASN B:424 , HIS B:454 , TYR B:456 , LYA B:513 , HOH B:544 , HOH B:717BINDING SITE FOR RESIDUE UMP B 512
09AC9SOFTWAREALA B:278 , SER B:281 , ILE B:306 , ASN B:310 , LEU B:390 , ASP B:416 , LEU B:419 , GLY B:420 , PHE B:423 , MET B:509 , SER B:510 , UMP B:512 , HOH B:524 , HOH B:545 , HOH B:552 , HOH B:556 , HOH B:566 , HOH B:595 , HOH B:718 , HOH B:737 , HOH B:763 , HOH B:804BINDING SITE FOR RESIDUE LYA B 513
10BC1SOFTWAREPHE B:14 , VAL B:15 , ALA B:16 , ASP B:37 , PHE B:38 , ARG B:39 , LEU B:41 , ARG B:42 , LEU B:80 , ARG B:83 , LEU B:123 , THR B:144 , NAP B:515 , HOH B:534 , HOH B:629 , HOH B:713BINDING SITE FOR RESIDUE LYA B 514
11BC2SOFTWAREARG A:305 , VAL B:15 , ALA B:16 , ILE B:23 , GLY B:24 , ASN B:27 , GLN B:28 , ILE B:29 , TRP B:31 , GLY B:66 , ARG B:67 , LYS B:68 , THR B:69 , SER B:72 , LEU B:88 , SER B:89 , ARG B:90 , THR B:91 , GLU B:102 , ASP B:103 , LEU B:123 , GLY B:125 , SER B:126 , PHE B:127 , TYR B:129 , GLU B:131 , THR B:154 , LYA B:514BINDING SITE FOR RESIDUE NAP B 515
12BC3SOFTWAREARG A:248 , ALA A:389 , PRO A:391 , HOH A:820 , ARG B:374BINDING SITE FOR RESIDUE EDO B 516
13BC4SOFTWAREPHE A:340 , GLY A:341 , ASN A:381 , SER A:383 , PHE B:340 , GLY B:341 , ASN B:381 , SER B:383BINDING SITE FOR RESIDUE EDO B 518

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:78 -Pro A:79
2Gly A:124 -Gly A:125
3Leu B:78 -Pro B:79
4Gly B:124 -Gly B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2H)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2H)

(-) 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:503
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:508
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503        
         A7ASX7_BABBO     4 SYEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
               SCOP domains d3k2ha1 A:4-187 automated matches                                                                                                                                                       -----------------d3k2ha2 A:205-511 automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhh....eeeeeehhhhhh..........eeeeee..........eee.hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeee.......ee.......eeeeee...ee....eeeeeeeee.hhh-----.hhhhhhh...................ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2h A   4 SYEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCK-----PPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183      |  -  |    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503        
                                                                                                                                                                                                                    190   196                                                                                                                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:503
 aligned with A7ASX7_BABBO | A7ASX7 from UniProtKB/TrEMBL  Length:511

    Alignment length:508
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503        
         A7ASX7_BABBO     4 SYEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCKTVFPDPPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
               SCOP domains d3k2hb1 B:4-187 automated matches                                                                                                                                                       -----------------d3k2hb2 B:205-511 automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------DHFR_1-3k2hB01 B:10-186                                                                                                                                                          -----------------------------------------Thymidylat_synt-3k2hB03 B:228-511                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) ------DHFR_1-3k2hB02 B:10-186                                                                                                                                                          -----------------------------------------Thymidylat_synt-3k2hB04 B:228-511                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ........eeeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhh.....eeeeehhhhhh...........eeeee.........eeee.hhhhhhhhhhhhh....eee..hhhhhhhhhhh....eeeeeee.......ee.......eeeeee...ee....eeeeeeeee.hhh-----.hhhhhhh...................ee..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2h B   4 SYEGCGDLTIFVAVALNKVIGHKNQIPWPHITHDFRFLRNGTTYIPPEVLSKNPDIQNVVIFGRKTYESIPKASLPLKNRINVILSRTVKEVPGCLVYEDLSTAIRDLRANVPHNKIFILGGSFLYKEVLDNGLCDKIYLTRLNKEYPGDTYFPDIPDTFEITAISPTFSTDFVSYDFVIYERKDCK-----PPFDQLLMTGTDISVPKPKYVACPGVRIRNHEEFQYLDILADVLSHGVLKPNRTGTDAYSKFGYQMRFDLSRSFPLLTTKKVALRSIIEELLWFIKGSTNGNDLLAKNVRIWELNGRRDFLDKNGFTDREEHDLGPIYGFQWRHFGAEYLDMHADYTGKGIDQLAEIINRIKTNPNDRRLIVCSWNVSDLKKMALPPCHCFFQFYVSDNKLSCMMHQRSCDLGLGVPFNIASYSILTAMVAQVCGLGLGEFVHNLADAHIYVDHVDAVTTQIARIPHPFPRLRLNPDIRNIEDFTIDDIVVEDYVSHPPIPMAMSA 511
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183      |  -  |    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503        
                                                                                                                                                                                                                    190   196                                                                                                                                                                                                                                                                                                                           

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2H)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)
(-)
Family: DHFR_1 (89)
1aDHFR_1-3k2hB01B:10-186
1bDHFR_1-3k2hB02B:10-186

(-) 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 | A7ASX73i3r 3kjr 3nrr

(-) Related Entries Specified in the PDB File

3i3r APO STRUCTURE RELATED ID: BABOA.01191.A RELATED DB: TARGETDB