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(-) Description

Title :  CATALYTIC INTERMEDIATE ANALOGUE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  T. Murakawa, Y. Machida, H. Hayashi
Date :  13 Feb 10  (Deposition) - 17 Nov 10  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Threonine Synthase, Plp, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Murakawa, Y. Machida, H. Hayashi
Product-Assisted Catalysis As The Basis Of The Reaction Specificity Of Threonine Synthase.
J. Biol. Chem. V. 286 2774 2011
PubMed-ID: 21084312  |  Reference-DOI: 10.1074/JBC.M110.186205

(-) Compounds

Molecule 1 - THREONINE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TTHA0491
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AN72Ligand/Ion(3E)-4-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}-2-OXOBUT-3-ENOIC ACID
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:60 , LYS A:61 , SER A:84 , THR A:85 , GLY A:86 , ASN A:87 , THR A:88 , PHE A:134 , VAL A:186 , GLY A:187 , ASN A:188 , ALA A:189 , GLY A:190 , ASN A:191 , ALA A:240 , ILE A:241 , GLU A:287 , THR A:317 , HOH A:365 , HOH A:377 , HOH A:388 , HOH A:392 , HOH A:430 , PO4 A:6265BINDING SITE FOR RESIDUE AN7 A 1001
2AC2SOFTWARELYS A:61 , THR A:88 , ASN A:154 , SER A:155 , ARG A:160 , ASN A:188 , HOH A:365 , AN7 A:1001BINDING SITE FOR RESIDUE PO4 A 6265
3AC3SOFTWAREPHE B:60 , LYS B:61 , SER B:84 , THR B:85 , GLY B:86 , ASN B:87 , THR B:88 , PHE B:134 , VAL B:186 , GLY B:187 , ASN B:188 , ALA B:189 , GLY B:190 , ASN B:191 , ALA B:240 , ILE B:241 , GLU B:287 , THR B:317 , GLY B:318 , HOH B:356 , HOH B:360 , HOH B:368 , HOH B:381 , HOH B:429 , PO4 B:6267BINDING SITE FOR RESIDUE AN7 B 1002
4AC4SOFTWARELYS B:61 , THR B:88 , PHE B:134 , ASN B:154 , SER B:155 , ARG B:160 , ASN B:188 , HOH B:356 , AN7 B:1002BINDING SITE FOR RESIDUE PO4 B 6267

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:36 -Pro A:37
2Gly B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AEX)

(-) 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:351
 aligned with Q5SL02_THET8 | Q5SL02 from UniProtKB/TrEMBL  Length:351

    Alignment length:351
                                    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       320       330       340       350 
         Q5SL02_THET8     1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
               SCOP domains d3aexa_ A: Threonine synthase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eee...hhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.........eeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aex A   1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
                                    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       320       330       340       350 


Chain B from PDB  Type:PROTEIN  Length:351
 aligned with Q5SL02_THET8 | Q5SL02 from UniProtKB/TrEMBL  Length:351

    Alignment length:351
                                    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       320       330       340       350 
         Q5SL02_THET8     1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
               SCOP domains d3aexb_ B: Threonine synthase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eee...hhhhhh...eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aex B   1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
                                    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       320       330       340       350
   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 3AEX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SL02_THET8 | Q5SL02)
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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 Related Entries

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UniProtKB/TrEMBL
        Q5SL02_THET8 | Q5SL02: 3aey

(-) Related Entries Specified in the PDB File

1uim CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, ORTHORHOMBIC CRYSTAL FORM
1uin CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, TRIGONAL CRYSTAL FORM
1v7c CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH A SUBSTRATE ANALOGUE