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(-) Description

Title :  CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM THERMUS THERMOPHILUS HB8, TRIGONAL 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 :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (2x),B (2x)
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 Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:84 , THR B:88 , SER B:155 , ARG B:160 , ASN B:188 , HOH B:1556BINDING SITE FOR RESIDUE SO4 B 1001
2AC2SOFTWAREARG A:229 , VAL A:231 , GLU A:232 , ARG A:233 , GLN A:250 , HOH A:1114BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREILE A:243 , GLY A:244 , ASN A:245 , HOH A:1073BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWARESER A:59 , PHE A:60 , LYS A:61 , ASN A:87 , VAL A:186 , 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:1008 , HOH A:1010 , HOH A:1044 , HOH A:1103BINDING SITE FOR RESIDUE PLP A 513
5AC5SOFTWAREPHE 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:1515 , HOH B:1516 , HOH B:1529BINDING SITE FOR RESIDUE PLP B 1513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 1UIN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UIN)

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

    Alignment length:350
                                    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
         P83823_THETH     2 RPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
               SCOP domains d1uina_ A: Threonine synthase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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..hhhhhhhhhh........ee.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uin A   2 RPPLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGLL 351
                                    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


Chain B from PDB  Type:PROTEIN  Length:346
 aligned with P83823_THETH | P83823 from UniProtKB/TrEMBL  Length:351

    Alignment length:347
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       
         P83823_THETH     4 PLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAGYVALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
               SCOP domains d1uinb_ B: Threonine synthase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------PALP-1uinB01 B:22-318                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------PALP-1uinB02 B:22-318                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh.................eee...hhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeeeee..-.hhhhhhhhhhh..eeeeee.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
                 1uin B   4 PLIERYRNLLPVSEKTPVISLLEGSTPLIPLKGPEEARKKGIRLYAKYEGLNPTGSFKDRGMTLAVSKAVEGGAQAVACASTGNTAASAAAYAARAGILAIVVLPAG-VALGKVAQSLVHGARIVQVEGNFDDALRLTQKLTEAFPVALVNSVNPHRLEGQKTLAFEVVDELGDAPHYHALPVGNAGNITAHWMGYKAYHALGKAKRLPRMLGFQAAGAAPLVLGRPVERPETLATAIRIGNPASWQGAVRAKEESGGVIEAVTDEEILFAYRYLAREEGIFCEPASAAAMAGVFKLLREGRLEPESTVVLTLTGHGLKDPATAERVAELPPPVPARLEAVAAAAGL 350
                                    13        23        33        43        53        63        73        83        93       103      |113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       
                                                                                                                                    110 |                                                                                                                                                                                                                                              
                                                                                                                                      112
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric 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: 1uim 1v7c

(-) Related Entries Specified in the PDB File

1uim ORTHORHOMBIC CRYSTAL FORM
1uiq COMPLEX WITH A SUBSTRATE ANALOGUE RELATED ID: TTK003000028.2 RELATED DB: TARGETDB