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(-) Description

Title :  LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND THE PHTALIMIDIC DERIVATIVE C00 IN MULTIPLE BINDING MODES
 
Authors :  R. Leone, S. Mangani, L. Cancian, M. P. Costi, R. Luciani, S. Ferrari
Date :  16 Jan 08  (Deposition) - 20 Jan 09  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structure Based Drug Design, Methyltransferase, Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mangani, L. Cancian, R. Leone, C. Pozzi, S. Lazzari, R. Luciani, S. Ferrari, M. P. Costi
Identification Of The Binding Modes Of N-Phenylphthalimides Inhibiting Bacterial Thymidylate Synthase Through X-Ray Crystallography Screening
J. Med. Chem. V. 54 5454 2011
PubMed-ID: 21696158  |  Reference-DOI: 10.1021/JM2005018

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKPTSD
    Expression System Strain: CHI 2913
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS CASEI
    Organism Taxid: 1582
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1C001Ligand/Ion2-(4-HYDROXYBIPHENYL-3-YL)-4-METHYL-1H-ISOINDOLE-1,3(2H)-DIONE
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1C002Ligand/Ion2-(4-HYDROXYBIPHENYL-3-YL)-4-METHYL-1H-ISOINDOLE-1,3(2H)-DIONE
2UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , ARG A:178 , ARG A:179 , LEU A:195 , CYS A:198 , HIS A:199 , GLN A:217 , ARG A:218 , SER A:219 , ALA A:220 , ASP A:221 , ASN A:229 , HIS A:259 , TYR A:261 , HOH A:334BINDING SITE FOR RESIDUE UMP A 317
2AC2SOFTWAREARG A:23 , ILE A:81 , TRP A:82 , TRP A:85 , LEU A:195 , LEU A:224 , GLY A:225 , PHE A:228 , ALA A:315BINDING SITE FOR RESIDUE C00 A 318

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_LACCA178-206  1A:178-206
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_LACCA178-206  2A:178-206

(-) Exons   (0, 0)

(no "Exon" information available for 3BYX)

(-) Sequences/Alignments

Asymmetric 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:313
 aligned with TYSY_LACCA | P00469 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:315
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
           TYSY_LACCA     1 MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTKKVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPDMTDFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLLNYDPYPAIKAPVA 315
               SCOP domains d3byxa_ A: Thymidylate synthase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3byxA00 A:1-315 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhh..........hhhhhh.--.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhee.....eehhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3byx A   1 MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTKKVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPDMTDFGHRSQ--PEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLLNYDPYPAIKAPVA 315
                                    10        20        30        40        50        60        70        80        90       100        |- |     120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
                                                                                                                                      109  |                                                                                                                                                                                                           
                                                                                                                                         112
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TYSY_LACCA | P00469)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_LACCA | P00469: 1bo7 1bo8 1bp0 1bp6 1bpj 1jmf 1jmg 1jmh 1jmi 1lca 1lcb 1lce 1nja 1njb 1njc 1njd 1nje 1tda 1tdb 1tdc 1thy 1tsl 1tsm 1tsv 1tsw 1tsx 1tsy 1tsz 1tvu 1tvv 1tvw 1vza 1vzb 1vzc 1vzd 1vze 2g86 2g89 2g8a 2g8d 2tdd 2tdm 3bnz 3bz0 3c06 3c0a 3ijz 3ik0 3ik1 4tms

(-) Related Entries Specified in the PDB File

1lce 1tsl 3bnz 3bz0 3c06 3c0a