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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP AND BW1843U89
 
Authors :  A. C. Anderson, R. H. O'Neil, T. S. Surti, R. M. Stroud
Date :  23 May 00  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Beta-Sheet, Protein-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. Anderson, R. H. O'Neil, T. S. Surti, R. M. Stroud
Approaches To Solving The Rigid Receptor Problem By Identifying A Minimal Set Of Flexible Residues During Ligand Docking.
Chem. Biol. V. 8 445 2001
PubMed-ID: 11358692  |  Reference-DOI: 10.1016/S1074-5521(01)00023-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    ChainsA, B, C, D
    EC Number2.1.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUETS-1.8
    Expression System StrainCHI-2913
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPNEUMOCYSTIS CARINII
    Organism Taxid4754

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1F894Ligand/IonS)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
2UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1F892Ligand/IonS)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
2UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1F892Ligand/IonS)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
2UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:26 , LEU A:170 , CYS A:173 , HIS A:174 , GLN A:198 , ARG A:199 , SER A:200 , ASP A:202 , GLY A:206 , ASN A:210 , HIS A:240 , TYR A:242 , F89 A:401 , HOH A:519 , ARG B:153 , ARG B:154 , HOH B:741BINDING SITE FOR RESIDUE UMP A 301
2AC2SOFTWAREARG A:153 , ARG A:154 , ARG B:26 , LEU B:170 , CYS B:173 , HIS B:174 , GLN B:198 , ARG B:199 , SER B:200 , ASP B:202 , ASN B:210 , HIS B:240 , TYR B:242 , F89 B:402 , HOH B:682 , HOH B:748BINDING SITE FOR RESIDUE UMP B 302
3AC3SOFTWAREARG C:26 , TYR C:113 , LEU C:170 , CYS C:173 , HIS C:174 , GLN C:198 , ARG C:199 , SER C:200 , ASP C:202 , GLY C:206 , ASN C:210 , HIS C:240 , TYR C:242 , F89 C:403 , HOH C:589 , ARG D:153 , ARG D:154BINDING SITE FOR RESIDUE UMP C 303
4AC4SOFTWAREARG C:153 , ARG C:154 , HOH C:756 , ARG D:26 , LEU D:170 , CYS D:173 , HIS D:174 , GLN D:198 , ARG D:199 , SER D:200 , ASP D:202 , ASN D:210 , HIS D:240 , TYR D:242 , F89 D:404 , HOH D:690BINDING SITE FOR RESIDUE UMP D 304
5AC5SOFTWAREPHE A:58 , GLY A:61 , GLU A:65 , HIS A:85 , ILE A:86 , TRP A:87 , ASN A:90 , LEU A:170 , ASP A:202 , LEU A:205 , GLY A:206 , PHE A:209 , SER A:296 , UMP A:301BINDING SITE FOR RESIDUE F89 A 401
6AC6SOFTWAREPHE B:58 , GLY B:61 , GLU B:65 , HIS B:85 , ILE B:86 , TRP B:87 , ASN B:90 , ASP B:202 , GLY B:206 , PHE B:209 , TYR B:242 , MET B:295 , ILE B:297 , UMP B:302 , HOH B:643BINDING SITE FOR RESIDUE F89 B 402
7AC7SOFTWAREPHE C:58 , GLY C:61 , GLU C:65 , HIS C:85 , ILE C:86 , TRP C:87 , ASN C:90 , LEU C:170 , ASP C:202 , LEU C:205 , GLY C:206 , PHE C:209 , TYR C:242 , SER C:296 , UMP C:303BINDING SITE FOR RESIDUE F89 C 403
8AC8SOFTWAREPHE D:58 , GLY D:61 , GLU D:65 , HIS D:85 , ILE D:86 , TRP D:87 , ASN D:90 , ASP D:202 , GLY D:206 , PHE D:209 , TYR D:242 , MET D:295 , ILE D:297 , UMP D:304BINDING SITE FOR RESIDUE F89 D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F28)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_PNECA153-181
 
 
 
  4A:153-181
B:153-181
C:153-181
D:153-181
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_PNECA153-181
 
 
 
  2A:153-181
B:153-181
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_PNECA153-181
 
 
 
  2-
-
C:153-181
D:153-181

(-) Exons   (0, 0)

(no "Exon" information available for 1F28)

(-) 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:295
 aligned with TYSY_PNECA | P13100 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           TYSY_PNECA     3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
               SCOP domains d1f28a_ A: Thymidylate synthase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f28A00 A:3-297 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee.....eeeeee....eeee.hhh..........hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeehhhhhhhhhhhhh......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f28 A   3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with TYSY_PNECA | P13100 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           TYSY_PNECA     3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
               SCOP domains d1f28b_ B: Thymidylate synthase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f28B00 B:3-297 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee.....eeeeee....eeee.hhh..........hhhhhhhhhhhhhh....hhhhhh..........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f28 B   3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     

Chain C from PDB  Type:PROTEIN  Length:295
 aligned with TYSY_PNECA | P13100 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           TYSY_PNECA     3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
               SCOP domains d1f28c_ C: Thymidylate synthase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f28C00 C:3-297 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee.....eeeeee....eeee.hhh..........hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f28 C   3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     

Chain D from PDB  Type:PROTEIN  Length:295
 aligned with TYSY_PNECA | P13100 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           TYSY_PNECA     3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
               SCOP domains d1f28d_ D: Thymidylate synthase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f28D00 D:3-297 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee.....eeeeee....eeee.hhh..........hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeee.........eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f28 D   3 NAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI 297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F28)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TYSY_PNECA | P13100)
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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_PNECA | P131001ci7

(-) Related Entries Specified in the PDB File

1ci7 1CI7 CONTAINS THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP AND CB3717