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(-) Description

Title :  CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, ORTHORHOMBIC CRYSTAL FORM
 
Authors :  R. Omi, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Jul 03  (Deposition) - 18 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plp-Dependent Enzyme, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Omi, G. Masaru, I. Miyahara, H. Mizuguchi, H. Hayashi, H. Kagamiyama, K. Hirotsu
Crystal Structures Of Threonine Synthase From Thermus Thermophilus Hb8: Conformational Change, Substrate Recognition, And Mechanism.
J. Biol. Chem. V. 278 46035 2003
PubMed-ID: 12952961  |  Reference-DOI: 10.1074/JBC.M308065200

(-) Compounds

Molecule 1 - THREONINE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HB8
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:60 , LYS A:61 , ASN A:87 , GLY A:187 , ASN A:188 , ALA A:189 , GLY A:190 , ASN A:191 , ALA A:240 , GLU A:287 , THR A:317 , GLY A:318 , HOH A:405 , HOH A:408 , HOH A:433BINDING SITE FOR RESIDUE PLP A 400
2AC2SOFTWAREPHE B:60 , LYS B:61 , ASN B:87 , VAL B:186 , GLY B:187 , ASN B:188 , ALA B:189 , GLY B:190 , ASN B:191 , ALA B:240 , GLU B:287 , THR B:317 , GLY B:318 , HOH B:1410 , HOH B:1412 , HOH B:1452 , HOH B:1528BINDING SITE FOR RESIDUE PLP B 1400

(-) SS Bonds  (0, 0)

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

(-) 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 1UIM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UIM)

(-) Exons   (0, 0)

(no "Exon" information available for 1UIM)

(-) 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:350
 aligned with P83823_THETH | P83823 from UniProtKB/TrEMBL  Length:351

    Alignment length:350
                                    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
         P83823_THETH     1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
               SCOP domains d1uima_ A: Threonine synthase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eee...hhhhhh...eeeeee.hhh....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uim A   1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
                                    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:350
 aligned with P83823_THETH | P83823 from UniProtKB/TrEMBL  Length:351

    Alignment length:350
                                    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
         P83823_THETH     1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
               SCOP domains d1uimb_ B: Threonine synthase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------PALP-1uimB01 B:22-318                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------PALP-1uimB02 B:22-318                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhh.................eee...hhhhhh...eeeeee.hhh....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhh........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uim B   1 MRPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
                                    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 1UIM)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PALP] (67)
(-)
Family: PALP (67)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83823_THETH | P83823)
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

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

UniProtKB/TrEMBL
        P83823_THETH | P83823: 1uin 1v7c

(-) Related Entries Specified in the PDB File

1uin TRIGONAL CRYSTAL FORM
1uiq COMPLEX WITH A SUBSTRATE ANALOGUE RELATED ID: TTK003000028.1 RELATED DB: TARGETDB