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(-) Description

Title :  CRYSTAL STRUCTURE OF ECTS/DUMP/THF COMPLEX
 
Authors :  T. A. Fritz, L. Liu, J. S. Finer-Moore, R. M. Stroud
Date :  06 Feb 02  (Deposition) - 03 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme Substrate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Fritz, L. Liu, J. S. Finer-Moore, R. M. Stroud
Tryptophan 80 And Leucine 143 Are Critical For The Hydride Transfer Step Of Thymidylate Synthase By Controlling Active Site Access.
Biochemistry V. 41 7021 2002
PubMed-ID: 12033935  |  Reference-DOI: 10.1021/BI012108C

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1CO33Ligand/IonCARBONATE ION
2CXM2Mod. Amino AcidN-CARBOXYMETHIONINE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5GOL1Ligand/IonGLYCEROL
6THG2Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE
7UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , HOH A:558 , HOH A:738BINDING SITE FOR RESIDUE CO3 A 803
02AC2SOFTWAREARG A:49 , GLY A:257 , HOH A:493BINDING SITE FOR RESIDUE CO3 A 804
03AC3SOFTWAREGLU A:223 , ARG A:225 , HIS A:255 , HOH A:744BINDING SITE FOR RESIDUE CO3 A 805
04AC4SOFTWAREARG A:21 , TYR A:94 , CYS A:146 , HIS A:147 , GLN A:165 , ARG A:166 , SER A:167 , CYS A:168 , ASP A:169 , ASN A:177 , HIS A:207 , TYR A:209 , THG A:303 , HOH A:412 , HOH A:432 , HOH A:658 , ARG B:126 , ARG B:127BINDING SITE FOR RESIDUE UMP A 302
05AC5SOFTWAREHIS A:51 , ILE A:79 , TRP A:80 , TRP A:83 , LEU A:143 , ASP A:169 , GLY A:173 , PHE A:176 , VAL A:262 , ALA A:263 , UMP A:302 , HOH A:419 , HOH A:442 , HOH A:448 , HOH A:467 , HOH A:551 , HOH A:575 , HOH A:597 , HOH A:615 , HOH A:625 , HOH A:646BINDING SITE FOR RESIDUE THG A 303
06AC6SOFTWARELEU A:116 , LYS A:120 , GLN A:191 , CYS A:192BINDING SITE FOR RESIDUE DTU A 800
07AC7SOFTWAREARG A:126 , ARG A:127 , ARG B:21 , CYS B:146 , HIS B:147 , GLN B:165 , ARG B:166 , SER B:167 , CYS B:168 , ASP B:169 , ASN B:177 , HIS B:207 , TYR B:209 , THG B:305 , HOH B:439 , HOH B:509BINDING SITE FOR RESIDUE UMP B 304
08AC8SOFTWAREILE B:79 , TRP B:83 , LEU B:143 , ASP B:169 , GLY B:173 , VAL B:262 , ALA B:263 , UMP B:304 , HOH B:461 , HOH B:480 , HOH B:569 , HOH B:737 , HOH B:749BINDING SITE FOR RESIDUE THG B 305
09AC9SOFTWAREPRO B:224 , ARG B:225 , PRO B:226 , ARG B:234 , ARG B:243 , GLU B:245 , ASP B:246 , HOH B:735BINDING SITE FOR RESIDUE DTT B 802
10BC1SOFTWAREGLN A:9 , GLN A:64 , ARG A:99 , HOH A:599BINDING SITE FOR RESIDUE GOL A 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_ECOLI126-154
 		  2A:126-154
B:126-154

(-) Exons   (0, 0)

(no "Exon" information available for 1KZI)

(-) 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:264
 aligned with TYSY_ECOLI | P0A884 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:264
                                    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    
           TYSY_ECOLI     1 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
               SCOP domains d1kzia_ A: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1kziA00 A:2-264 Thymidylate Synthase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kzi A   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            |                                                                                                                                                                                                                                                                       
                            1-CXM                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with TYSY_ECOLI | P0A884 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:264
                                    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    
           TYSY_ECOLI     1 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
               SCOP domains d1kzib_ B: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1kziB00 B:2-264 Thymidylate Synthase, chain A                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) Thymidylat_synt-1kziB01 B:1-264                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) Thymidylat_synt-1kziB02 B:1-264                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh....hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kzi B   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            1-CXM
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Thymidylat_synt] (68)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TYSY_ECOLI | P0A884)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1kzi
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  TYSY_ECOLI | P0A884
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  2.1.1.45
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_ECOLI | P0A884: 1aiq 1ajm 1an5 1aob 1axw 1bdu 1bid 1bjg 1bq1 1bq2 1ddu 1dna 1ev5 1ev8 1evf 1evg 1f4b 1f4c 1f4d 1f4e 1f4f 1f4g 1ffl 1fwm 1jg0 1jtq 1jtu 1jut 1kce 1kzj 1nce 1qqq 1syn 1tdu 1tjs 1tlc 1tls 1trg 1tsd 1tsn 1tys 1zpr 2a9w 2bbq 2ftn 2fto 2ftq 2g8x 2kce 2tsc 2vet 2vf0 3b5b 3b9h 3bfi 3bgx 3bhl 3bhr 3tms 4f2v 4gev 4isk 4knz

(-) Related Entries Specified in the PDB File

1kzj 1KZJ CONTAINS THE SAME PROTEIN