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(-) Description

Title :  CRYSTAL STRUCTURE OF THREONINE SYNTHASE FROM AQUIFEX AEOLICUS VF5
 
Authors :  H. Mizutani, N. Kunishima
Date :  11 Sep 08  (Deposition) - 21 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Threonine Synthase, Plp Dependent Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of Threonine Synthase From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THREONINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THRC2, AQ_425
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:61 , PHE A:62 , LYS A:63 , ASN A:89 , VAL A:188 , GLY A:189 , ASN A:190 , ALA A:191 , GLY A:192 , ASN A:193 , ALA A:242 , GLU A:289 , THR A:319 , GLY A:320 , HOH A:1119 , HOH A:1157 , HOH A:1198BINDING SITE FOR RESIDUE PLP A1101
2AC2SOFTWAREPHE B:62 , LYS B:63 , ASN B:89 , VAL B:188 , GLY B:189 , ASN B:190 , ALA B:191 , GLY B:192 , ASN B:193 , ALA B:242 , GLU B:289 , THR B:319 , GLY B:320 , HOH B:1129 , HOH B:1170 , HOH B:1172BINDING SITE FOR RESIDUE PLP B1102
3AC3SOFTWARESER C:61 , PHE C:62 , LYS C:63 , ASN C:89 , VAL C:188 , GLY C:189 , ASN C:190 , ALA C:191 , GLY C:192 , ASN C:193 , ALA C:242 , GLU C:289 , THR C:319 , GLY C:320 , HOH C:1111 , HOH C:1148 , HOH C:1176BINDING SITE FOR RESIDUE PLP C1103
4AC4SOFTWARESER D:61 , PHE D:62 , LYS D:63 , ASN D:89 , VAL D:188 , GLY D:189 , ASN D:190 , ALA D:191 , GLY D:192 , ASN D:193 , ALA D:242 , GLU D:289 , THR D:319 , GLY D:320 , HOH D:1125 , HOH D:1167 , HOH D:1177BINDING SITE FOR RESIDUE PLP D1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZSJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZSJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZSJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZSJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZSJ)

(-) 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 O66740_AQUAE | O66740 from UniProtKB/TrEMBL  Length:352

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
         O66740_AQUAE     3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
               SCOP domains d2zsja_ A: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eeehhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhh...eee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsj A   3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with O66740_AQUAE | O66740 from UniProtKB/TrEMBL  Length:352

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
         O66740_AQUAE     3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
               SCOP domains d2zsjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eeehhhhhhhhh...eeeeee.hhh....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh....eee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsj B   3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352


Chain C from PDB  Type:PROTEIN  Length:350
 aligned with O66740_AQUAE | O66740 from UniProtKB/TrEMBL  Length:352

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
         O66740_AQUAE     3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
               SCOP domains d2zsjc_ C: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.................eeehhhhhhhhh...eeeeee.hhh....hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhh...eee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsj C   3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352


Chain D from PDB  Type:PROTEIN  Length:348
 aligned with O66740_AQUAE | O66740 from UniProtKB/TrEMBL  Length:352

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
         O66740_AQUAE     3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
               SCOP domains d2zsjd_ D: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------PALP-2zsjD01 D:24-320                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------PALP-2zsjD02 D:24-320                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------PALP-2zsjD03 D:24-320                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------PALP-2zsjD04 D:24-320                                                                                                                                                                                                                                                                                    -------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhh.................eeehhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeeeeee..--hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh.......eeeeeee...hhhhhh.........hhhhh.....hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh....eee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsj D   3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKG--AIGKLSQAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPITVPPDFDEVVKVLGF 352
                                    12        22        32        42        52        62        72        82        92       102       112  |    122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
                                                                                                                                       112  |                                                                                                                                                                                                                                             
                                                                                                                                          115
   Legend:   → Mismatch (orange background)
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    → 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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZSJ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: PALP] (67)
(-)
Family: PALP (67)
(-)
Aquifex aeolicus (1)
1aPALP-2zsjD01D:24-320
1bPALP-2zsjD02D:24-320
1cPALP-2zsjD03D:24-320
1dPALP-2zsjD04D:24-320

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O66740_AQUAE | O66740)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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