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(-) Description

Title :  CRYSTAL STRUCTURE OF T.TH. HB8 THREONINE DEAMINASE
 
Authors :  M. Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi
Date :  27 Mar 04  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Threonine Deaminase Catabolic, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto
Crystal Structure Of T. Th. Hb8 Threonine Deaminase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THREONINE DEAMINASE
    Chains: A, B, C, D
    EC Number: 4.3.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: THREONINE DEHYDRATASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:203 , ALA A:207 , ASP A:209 , HOH A:1067 , HOH A:1223 , HOH A:1231BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREGLU D:203 , ALA D:207 , ASP D:209BINDING SITE FOR RESIDUE CA D 2002
3AC3SOFTWAREGLU B:203 , ALA B:207 , ASP B:209 , HOH B:1012BINDING SITE FOR RESIDUE CA B 2003
4AC4SOFTWAREGLU C:203 , ALA C:207 , ASP C:209 , HOH C:1063BINDING SITE FOR RESIDUE CA C 2004
5AC5SOFTWAREPHE A:50 , LYS A:51 , ASN A:75 , PRO A:176 , GLY A:178 , GLY A:179 , GLY A:180 , GLY A:181 , LEU A:182 , GLU A:277 , THR A:279 , SER A:303 , GLY A:304 , HOH A:1019 , HOH A:1109 , HOH A:1175BINDING SITE FOR RESIDUE PLP A 413
6AC6SOFTWAREPHE B:50 , LYS B:51 , ASN B:75 , PRO B:176 , VAL B:177 , GLY B:178 , GLY B:179 , GLY B:180 , GLY B:181 , LEU B:182 , GLU B:277 , THR B:279 , SER B:303 , HOH B:1001 , HOH B:1129BINDING SITE FOR RESIDUE PLP B 913
7AC7SOFTWAREPHE C:50 , LYS C:51 , ASN C:75 , PRO C:176 , GLY C:178 , GLY C:179 , GLY C:180 , GLY C:181 , LEU C:182 , GLU C:277 , THR C:279 , SER C:303 , HOH C:1039 , HOH C:1043BINDING SITE FOR RESIDUE PLP C 1413
8AC8SOFTWAREPHE D:50 , LYS D:51 , ASN D:75 , PRO D:176 , GLY D:178 , GLY D:179 , GLY D:180 , GLY D:181 , LEU D:182 , VAL D:233 , GLU D:277 , THR D:279 , SER D:303 , GLY D:304 , HOH D:1008 , HOH D:1011 , HOH D:1234BINDING SITE FOR RESIDUE PLP D 1913

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VE5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VE5)

(-) Exons   (0, 0)

(no "Exon" information available for 1VE5)

(-) 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:308
 aligned with Q5SLL4_THET8 | Q5SLL4 from UniProtKB/TrEMBL  Length:311

    Alignment length:310
                                    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
         Q5SLL4_THET8     2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMPEDASPYKKACARAYGAEVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
               SCOP domains d1ve5a1 A:2-311 Threonine deaminase                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeehhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee....--.hhhhhhhhh..eee.......hhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh............hhhhh.......hhhhhhhhh.eeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve5 A   2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMPED--PYKKACARAYGAEVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
                                    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
                                                                                                                           98  |                                                                                                                                                                                                                  
                                                                                                                             101                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q5SLL4_THET8 | Q5SLL4 from UniProtKB/TrEMBL  Length:311

    Alignment length:310
                                    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
         Q5SLL4_THET8     2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMPEDASPYKKACARAYGAEVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
               SCOP domains d1ve5b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....ee.hhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.eeee...------hhhhhhhh.eee.-------hhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh............hhhhh......hhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve5 B   2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMP------KKACARAYGAEVV-------NREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
                                    11        21        31        41        51        61        71        81        91    |    - |     111   |     - |     131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
                                                                                                                         96    103         115     123                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with Q5SLL4_THET8 | Q5SLL4 from UniProtKB/TrEMBL  Length:311

    Alignment length:310
                                    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
         Q5SLL4_THET8     2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMPEDASPYKKACARAYGAEVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
               SCOP domains d1ve5c_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....ee.hhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhh.eee.------------------------------------hhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhh.............hhhhh.......hhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve5 C   2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALV------------------------------------ALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
                                    11        21        31        41        51        61        71        81        91 |       -         -         -       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
                                                                                                                      93                                  130                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:280
 aligned with Q5SLL4_THET8 | Q5SLL4 from UniProtKB/TrEMBL  Length:311

    Alignment length:310
                                    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
         Q5SLL4_THET8     2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMPEDASPYKKACARAYGAEVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
               SCOP domains d1ve5d_ D: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------PALP-1ve5D01 D:14-304                                                                                                                                                                                                                                                                              ------- Pfam domains (1)
           Pfam domains (2) ------------PALP-1ve5D02 D:14-304                                                                                                                                                                                                                                                                              ------- Pfam domains (2)
           Pfam domains (3) ------------PALP-1ve5D03 D:14-304                                                                                                                                                                                                                                                                              ------- Pfam domains (3)
           Pfam domains (4) ------------PALP-1ve5D04 D:14-304                                                                                                                                                                                                                                                                              ------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeehhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh.eeeee..------------------------------.hhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh............hhhhh.......hhhhhhhhh.eeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve5 D   2 PSLQDLYAAFRRIAPYTHRTPLLTSRLLDGLLGKRLLLKAEHLQKTGSFKARGALSKALALENPKGLLAVSSGNHAQGVAYAAQVLGVKALVVMP------------------------------VARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMGVFPGAVLAPVGGGGLLAGLATAVKALSPTTLVLGVEPEAADDAKRSLEAGRILRLEAPPRTRADGVRTLSLGERTFPILRERVDGILTVSEEALLEAERLLFTRTKQVVEPTGALPLAAVLEHGARLPQTLALLLSGGNRDFSP 311
                                    11        21        31        41        51        61        71        81        91    |    -         -         -     | 131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
                                                                                                                         96                            127
   Legend:   → Mismatch (orange background)
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  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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VE5)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SLL4_THET8 | Q5SLL4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    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.

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