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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM BURKHOLDERIA THAILANDENSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  22 Dec 11  (Deposition) - 25 Jan 12  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ssgcid, Thymidylate Synthase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: THYA, BTH_I1680
    Organism Scientific: BURKHOLDERIA THAILANDENSIS
    Organism Taxid: 271848
    Strain: E264/ATCC 700388/DSM 13276/CIP 106301
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:189 , CYS A:192 , ARG A:214 , SER A:215 , HIS A:255 , TYR A:257 , ARG D:172 , ARG D:173BINDING SITE FOR RESIDUE CIT A 400
2AC2SOFTWAREALA A:65 , ARG A:67 , ASP A:104 , VAL A:108 , HOH A:1030BINDING SITE FOR RESIDUE EDO A 324
3AC3SOFTWAREALA A:74 , LEU A:75 , GLU A:302 , PRO A:303 , HOH A:430BINDING SITE FOR RESIDUE EDO A 325
4AC4SOFTWAREGLU A:143 , TYR D:116 , HIS D:152BINDING SITE FOR RESIDUE EDO A 326
5AC5SOFTWAREARG B:214 , SER B:215 , HIS B:255 , TYR B:257 , ARG C:172 , ARG C:173 , HOH C:1136BINDING SITE FOR RESIDUE CIT B 400
6AC6SOFTWAREALA B:123 , ASP B:124 , ALA B:125 , GLN B:126 , HOH B:349 , HOH B:674 , PRO C:94BINDING SITE FOR RESIDUE EDO B 324
7AC7SOFTWAREARG B:172 , ARG B:173 , LEU C:189 , CYS C:192 , ARG C:214 , SER C:215 , HIS C:255 , TYR C:257BINDING SITE FOR RESIDUE CIT C 400
8AC8SOFTWAREARG C:204 , ARG C:245 , HOH C:1084BINDING SITE FOR RESIDUE EDO C 324
9AC9SOFTWARETRP A:179 , GLN D:157 , ASP D:160 , CYS D:161 , ARG D:173 , LEU D:175 , HOH D:385BINDING SITE FOR RESIDUE EDO D 324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V8H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V8H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V8H)

(-) Exons   (0, 0)

(no "Exon" information available for 3V8H)

(-) 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:312
 aligned with Q2SXY2_BURTA | Q2SXY2 from UniProtKB/TrEMBL  Length:323

    Alignment length:314
                                    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    
         Q2SXY2_BURTA     1 MKQYLDLVRTILDTGTWQSNRTGIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVGYRHH 314
               SCOP domains d3v8ha_ A: automated   matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee..--...eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhh.............hhhhhhheeeeeeee..hhhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee....eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhh....hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8h A   1 MKQYLDLVRTILDTGTWQSN--GIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVGYRHH 314
                                    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    
                                              20 23                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Q2SXY2_BURTA | Q2SXY2 from UniProtKB/TrEMBL  Length:323

    Alignment length:314
                                    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    
         Q2SXY2_BURTA     1 MKQYLDLVRTILDTGTWQSNRTGIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVGYRHH 314
               SCOP domains d3v8hb_ B: automated    matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee..---..eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhh.............hhhhhhheeeeeeee..hhhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee....eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhh....hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8h B   1 MKQYLDLVRTILDTGTWQSN---IRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVGYRHH 314
                                    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    
                                              20  24                                                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with Q2SXY2_BURTA | Q2SXY2 from UniProtKB/TrEMBL  Length:323

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q2SXY2_BURTA     2 KQYLDLVRTILDTGTWQSNRTGIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVG 310
               SCOP domains d3v8hc_ C: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhheee.......eeeeeeeeeeee......------.hhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhh.............hhhhhhheeeeeeee..hhhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhhhhh......eee..hhhhh........eeeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee...---------------.eeee.....hhhhhh....hhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8h C   2 KQYLDLVRTILDTGTWQSNRTGIRTIGIPGAMLRFDLQQGFP------LAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQ---------------PRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVG 310
                                    11        21        31        41 |      51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        |-         -    |  281       291       301         
                                                                    43     50                                                                                                                                                                                                               260             276                                  


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with Q2SXY2_BURTA | Q2SXY2 from UniProtKB/TrEMBL  Length:323

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q2SXY2_BURTA     2 KQYLDLVRTILDTGTWQSNRTGIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQLEREPFESPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVG 310
               SCOP domains d3v8hd_ D: automa      ted matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhee.------.eeeeeeeeeeee......------.hhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhh.............hhhhhhheeeeeeee..hhhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhhhhh......eee..hhhhh........eeeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhh-------..eeee.....hhhhhh....hhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8h D   2 KQYLDLVRTILDTGTWQ------RTIGIPGAMLRFDLQQGFP------LAFKSAIGELVGFLRATRSAAEFRALGCKVWDANANENAQWLANPYRRGADDLGDVYGVQWRRWPGYKVLDAHADAQIADATSRGFRIVARFEEGGADKVLLHKAIDQLRDCLDTIVRDPSSRRILFHGWNPAVLDEIALPACHLLYQFLPNVERREISLCLYIRSNDVGLGTPFNLAEGAALLTLVGRLTGYSPRWFTYFIGDAHIYENQLDMLKQQ-------SPRLELAERVPDYAKTGKYEPQWLERVEPSDFTLVG 310
                                    11      |  -   |    31        41 |      51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     |   -   |   281       291       301         
                                           18     25                43     50                                                                                                                                                                                                                      267     275
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V8H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V8H)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q2SXY2_BURTA | Q2SXY2)
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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  3v8h
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