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(-) Description

Title :  CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM YEAST
 
Authors :  M. Garrido-Franco, S. Ehlert, A. Messerschmidt, S. Marinkovic, R. Hub B. Laber, G. P. Bourenkov, T. Clausen
Date :  11 Dec 01  (Deposition) - 24 Apr 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Threonine Synthesis, Pyridoxal 5-Phosphate, Beta-Family, Monomer, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Garrido-Franco, S. Ehlert, A. Messerschmidt, S. Marinkovic', R. Huber, B. Laber, G. P. Bourenkov, T. Clausen
Structure And Function Of Threonine Synthase From Yeast.
J. Biol. Chem. V. 277 12396 2002
PubMed-ID: 11756443  |  Reference-DOI: 10.1074/JBC.M108734200

(-) Compounds

Molecule 1 - THREONINE SYNTHASE
    ChainsA, B
    EC Number4.2.99.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:123 , LYS A:124 , ASP A:163 , SER A:276 , GLY A:277 , ASN A:278 , PHE A:279 , GLY A:280 , ASP A:281 , ALA A:330 , HIS A:422 , THR A:449 , ALA A:450 , HOH A:1401 , HOH A:1454 , HOH A:1548BINDING SITE FOR RESIDUE PLP A 1400
2AC2SOFTWAREPHE B:123 , LYS B:124 , ASP B:163 , SER B:276 , GLY B:277 , ASN B:278 , PHE B:279 , GLY B:280 , ASP B:281 , ALA B:330 , HIS B:422 , THR B:449 , ALA B:450 , HOH B:1405 , HOH B:1442 , HOH B:1572BINDING SITE FOR RESIDUE PLP B 1400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KL7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:413 -Pro A:414
2Asn B:413 -Pro B:414

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KL7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.THRC_YEAST114-128
 
  2A:114-128
B:114-128
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.THRC_YEAST114-128
 
  1A:114-128
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.THRC_YEAST114-128
 
  1-
B:114-128

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR053W1YCR053W.1III:216693-2182371545THRC_YEAST1-5145142A:2-512 (gaps)
B:2-512 (gaps)
511
511

(-) 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:509
 aligned with THRC_YEAST | P16120 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:511
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
           THRC_YEAST     2 PNASQVYRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAIMRLYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTGRISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHNVGAVNSINWARILAQMTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKMGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDVLPEELKKLSTLKKKLKFIERADVELVKNAIEEELAKM 512
               SCOP domains d1kl7a_ A: Threonine synthase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kl7A01 A:2-94 threonine synthase, domain 1, chain A                                         1kl7A02                  1kl7A03 A:120-242,A:477-511  [code=3.40.50.1100, no name defined]                                                          1kl7A02 A:95-119,A:243-476  [code=3.40.50.1100, no name defined]                                                                                                                                                                          1kl7A03 A:120-242,A:477-511        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.........hhhhhhhhh.......ee.......hhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhh..........ee.........eeeee.........hhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhh....eeeeeeee....hhhhhhhhhhh....eeeeee..hh.hhh.............--.........hhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhh.....eeeee...hhhhhhhhhheee.........hhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhheee.hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhh.....ee....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------DEHYDRATASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-512 (gaps) UniProt: 1-514 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 1kl7 A   2 PNASQVYRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAImRLYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTGRISPIQEEQmTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFN--HNVGAVNSINWARILAQmTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKmGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPAmDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDVLPEELKKLSTLKKKLKFIERADVELVKNAIEEELAKm 512
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511|
                                                                                           66-MSE                                                                                                                            197-MSE                           231  |              251-MSE                                 291-MSE                                 331-MSE                                                                                                                                                                              512-MSE
                                                                                                                                                                                                                                                                  234                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:509
 aligned with THRC_YEAST | P16120 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:511
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
           THRC_YEAST     2 PNASQVYRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAIMRLYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTGRISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHNVGAVNSINWARILAQMTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKMGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDVLPEELKKLSTLKKKLKFIERADVELVKNAIEEELAKM 512
               SCOP domains d1kl7b_ B: Threonine synthase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kl7B01 B:2-94 threonine synthase, domain 1, chain A                                         1kl7B02                  1kl7B03 B:120-242,B:477-511  [code=3.40.50.1100, no name defined]                                                          1kl7B02 B:95-119,B:243-476  [code=3.40.50.1100, no name defined]                                                                                                                                                                          1kl7B03 B:120-242,B:477-511        - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------PALP-1kl7B01 B:91-448                                                                                                                                                                                                                                                                                                                                                 ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------PALP-1kl7B02 B:91-448                                                                                                                                                                                                                                                                                                                                                 ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......ee.........hhhhhhhhh.......ee.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..........ee.........eeeee.........hhhhhhhhhhhhhhhhhhhhh..........eeeee...hhhhhhhhhhh......eeeeee....hhhhhhhhhhh....eeeeee..hh.hhh.............--..eee....hhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhh.....eeeee...hhhhhhhhhheee.........hhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhheee.hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhh.....ee....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------DEHYDRATASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-512 (gaps) UniProt: 1-514 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 1kl7 B   2 PNASQVYRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAImRLYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTGRISPIQEEQmTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFN--HNVGAVNSINWARILAQmTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKmGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPAmDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDVLPEELKKLSTLKKKLKFIERADVELVKNAIEEELAKm 512
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511|
                                                                                           66-MSE                                                                                                                            197-MSE                           231  |              251-MSE                                 291-MSE                                 331-MSE                                                                                                                                                                              512-MSE
                                                                                                                                                                                                                                                                  234                                                                                                                                                                                                                                                                                      

   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 Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THRC_YEAST | P16120)
molecular function
    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: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.

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