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(-) Description

Title :  STRUCTURE OF THREONINE SYNTHASE FROM ARABIDOPSIS THALIANA
 
Authors :  K. Thomazeau, G. Curien, R. Dumas, V. Biou
Date :  04 Aug 00  (Deposition) - 02 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Threonine Biosynthesis, Plp Enzyme, S-Adenosyl-Methionine, Allostery (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Thomazeau, G. Curien, R. Dumas, V. Biou
Crystal Structure Of Threonine Synthase From Arabidopsis Thaliana
Protein Sci. V. 10 638 2001
PubMed-ID: 11344332  |  Reference-DOI: 10.1110/PS.44301

(-) Compounds

Molecule 1 - THREONINE SYNTHASE
    Cellular Location: CHLOROPLAST
    Chains: A, B
    EC Number: 4.2.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: THRC_ARATH
    Expression System Plasmid: PET23 THRC_ARATH
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET23
    Expression System Vector Type: PLASMIDE
    Gene: NUCLEAR
    Organelle: CHLOROPLAST
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: MATURE ENZYME IS WITHOUT TRANSIT PEPTIDE
    Plasmid: PET23

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric/Biological Unit (2, 26)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2MSO2Mod. Amino AcidSELENOMETHIONINE SELENOXIDE

(-) Sites  (0, 0)

(no "Site" information available for 1E5X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E5X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:101 -Pro A:102
2Trp B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E5X)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.THRC1_ARATH193-207
 		  2A:153-167
B:153-167

(-) Exons   (0, 0)

(no "Exon" information available for 1E5X)

(-) 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:451
 aligned with THRC1_ARATH | Q9S7B5 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:477
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       
          THRC1_ARATH    50 IETAVKPPHRTEDNIRDEARRNRSNAVNPFSAKYVPFNAAPGSTESYSLDEIVYRSRSGGLLDVEHDMEALKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVSAFEGNSNLFWAERFGKQFLGMNDLWVKHCGISHTGSFKDLGMTVLVSQVNRLRKMKRPVVGVGCASTGDTSAALSAYCASAGIPSIVFLPANKISMAQLVQPIANGAFVLSIDTDFDGCMKLIREITAELPIYLANSLNSLRLEGQKTAAIEILQQFDWQVPDWVIVPGGNLGNIYAFYKGFKMCQELGLVDRIPRMVCAQAANANPLYLHYKSGWKDFKPMTASTTFASAIQIGDPVSIDRAVYALKKCNGIVEEATEEELMDAMAQADSTGMFICPHTGVALTALFKLRNQGVIAPTDRTVVVSTAHGLKFTQSKIDYHSNAIPDMACRFSNPPVDVKADFGAVMDVLKSYLGSNTLTS 526
               SCOP domains d1e5xa_ A: Threoni      ne synthase                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..------.......eeeee...................----..eeeeehhhhhhh.hhhhhhhhhhh............hhhhhhhh....hhhhh.........eeehhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh...............eeee....hhhhhhhh.......----------------..hhhhhhhhhhh...eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...................hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------DEHYDRATASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5x A  10 IETAVKPPHRTEDNIRDE------NAVNPFSAKYVPFNAAPGSTESYSLDEIVYR----GLLDVEHDmEALKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVSAFEGNSNLFWAERFGKQFLGmNDLWVKHCGISHTGSFKDLGmTVLVSQVNRLRKmKRPVVGVGCASTGDTSAALSAYCASAGIPSIVFLPANKISmAQLVQPIANGAFVLSIDTDFDGCmKLIREITAELPIYLANSLNSLRLEGQKTAAIEILQQFDWQVPDWVIVPGGNLGNIYAFYKGFKmCQELGLVDRIPRmVCAQAANANPLYLHYKSGWKDFKP----------------VSIDRAVYALKKCNGIVEEATEEELmDAmAQADSTGmFICPHTGVALTALFKLRNQGVIAPTDRTVVVSTAHGLKFTQSKIDYHSNAIPDmACRFSNPPVDVKADFGAVmDVLKSYLGSNTLTS 486
                                    19       | -    |   39        49        59    |   69       |79        89        99       109       119       129       139      |149       159       169       179|      189       199       209       219 |     229       239     | 249       259       269       279       289       299       309       319  |    329       339      |  -         -   |   369       379       389 |     399       409       419       429       439       449   |   459       469  |    479       
                                            27     34                            64   69      77-MSE                                                              146-MSE              167-MSE      180-MSE                                  221-MSE                 245-MSE                                                         309-MSO      322-MSE                 346              363                      388-MSE    399-MSE                                               453-MSE            472-MSE          
                                                                                                                                                                                                                                                                                                                                                                                                                       391-MSE                                                                                           


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with THRC1_ARATH | Q9S7B5 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:463
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516   
          THRC1_ARATH    57 PHRTEDNIRDEARRNRSNAVNPFSAKYVPFNAAPGSTESYSLDEIVYRSRSGGLLDVEHDMEALKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVSAFEGNSNLFWAERFGKQFLGMNDLWVKHCGISHTGSFKDLGMTVLVSQVNRLRKMKRPVVGVGCASTGDTSAALSAYCASAGIPSIVFLPANKISMAQLVQPIANGAFVLSIDTDFDGCMKLIREITAELPIYLANSLNSLRLEGQKTAAIEILQQFDWQVPDWVIVPGGNLGNIYAFYKGFKMCQELGLVDRIPRMVCAQAANANPLYLHYKSGWKDFKPMTASTTFASAIQIGDPVSIDRAVYALKKCNGIVEEATEEELMDAMAQADSTGMFICPHTGVALTALFKLRNQGVIAPTDRTVVVSTAHGLKFTQSKIDYHSNAIPDMACRFSNPPVDVKADFGAVMDVLKSYL 519
               SCOP domains d1e5xb_ B:         Threonine synthase                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.--------.....eeeee.................------..eeeeehhhhhh..hhhhhhhhhhh............hhhhhhhh....hhhhh.........eeehhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh...............eeee....hhhhhhhh.......----------------..hhhhhhhhhhh...eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------DEHYDRATASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e5x B  17 PHRTEDNIRDE--------VNPFSAKYVPFNAAPGSTESYSLDEIV------GLLDVEHDmEALKRFDGAYWRDLFDSRVGKSTWPYGSGVWSKKEWVLPEIDDDDIVSAFEGNSNLFWAERFGKQFLGmNDLWVKHCGISHTGSFKDLGmTVLVSQVNRLRKmKRPVVGVGCASTGDTSAALSAYCASAGIPSIVFLPANKISmAQLVQPIANGAFVLSIDTDFDGCmKLIREITAELPIYLANSLNSLRLEGQKTAAIEILQQFDWQVPDWVIVPGGNLGNIYAFYKGFKmCQELGLVDRIPRmVCAQAANANPLYLHYKSGWKDFKP----------------VSIDRAVYALKKCNGIVEEATEEELmDAmAQADSTGmFICPHTGVALTALFKLRNQGVIAPTDRTVVVSTAHGLKFTQSKIDYHSNAIPDmACRFSNPPVDVKADFGAVmDVLKSYL 479
                                    26|       36        46        56     |   -  |     76|       86        96       106       116       126       136       146       156       166|      176   |   186       196       206       216    |  226       236       246       256       266       276       286       296       306  |    316     | 326       336       346         -      |366       376       386 |  |  396  |    406       416       426       436       446      |456       466     | 476   
                                     27       36                        62     69      77-MSE                                                              146-MSE              167-MSE      180-MSE                                  221-MSE                 245-MSE                                                         309-MSO      322-MSE                 346              363                      388-MSE    399-MSE                                               453-MSE            472-MSE   
                                                                                                                                                                                                                                                                                                                                                                                                                391-MSE
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1E5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E5X)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THRC1_ARATH | Q9S7B5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004795    threonine synthase activity    Catalysis of the reaction: O-phospho-L-homoserine + H2O = L-threonine + phosphate.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009088    threonine biosynthetic process    The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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        THRC1_ARATH | Q9S7B5: 2c2b 2c2g

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