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(-) Description

Title :  THIAMIN PHOSPHATE SYNTHASE
 
Authors :  H. -J. Chiu, J. J. Reddick, T. P. Begley, S. E. Ealick
Date :  09 Mar 99  (Deposition) - 18 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thiamin Biosynthesis, Tim Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Chiu, J. J. Reddick, T. P. Begley, S. E. Ealick
Crystal Structure Of Thiamin Phosphate Synthase From Bacillus Subtilis At 1. 25 A Resolution.
Biochemistry V. 38 6460 1999
PubMed-ID: 10350464  |  Reference-DOI: 10.1021/BI982903Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (THIAMIN PHOSPHATE SYNTHASE)
    Chains: A, B
    EC Number: 2.5.1.3
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: DE3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2POP2Ligand/IonPYROPHOSPHATE 2-
3TPS2Ligand/IonTHIAMIN PHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2POP1Ligand/IonPYROPHOSPHATE 2-
3TPS1Ligand/IonTHIAMIN PHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2POP1Ligand/IonPYROPHOSPHATE 2-
3TPS1Ligand/IonTHIAMIN PHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:93 , ASP A:112 , POP A:2003 , HOH A:3020 , HOH A:3051BINDING SITE FOR RESIDUE MG A 2005
02AC2SOFTWAREASP B:93 , ASP B:112 , POP B:2004 , HOH B:3022 , HOH B:3057BINDING SITE FOR RESIDUE MG B 2006
03AC3SOFTWARETYR A:29 , ILE A:31 , GLN A:57 , ARG A:59 , ASN A:92 , HIS A:107 , SER A:130 , THR A:156 , THR A:158 , ILE A:186 , GLY A:188 , MET A:207 , ILE A:208 , SER A:209 , POP A:2003 , HOH A:3001 , HOH A:3002 , HOH A:3063 , HOH A:3144BINDING SITE FOR RESIDUE TPS A 2001
04AC4SOFTWARETYR B:29 , ILE B:31 , GLN B:57 , ARG B:59 , ASN B:92 , HIS B:107 , SER B:130 , THR B:156 , THR B:158 , LYS B:159 , ILE B:186 , GLY B:188 , MET B:207 , ILE B:208 , SER B:209 , POP B:2004 , HOH B:3003 , HOH B:3013 , HOH B:3169BINDING SITE FOR RESIDUE TPS B 2002
05AC5SOFTWAREARG A:59 , LYS A:61 , ASN A:92 , ASP A:93 , GLY A:109 , ASP A:112 , SER A:130 , LYS A:159 , TPS A:2001 , MG A:2005 , HOH A:3020 , HOH A:3027 , HOH A:3051 , HOH A:3062 , HOH A:3098 , HOH A:3108BINDING SITE FOR RESIDUE POP A 2003
06AC6SOFTWAREARG B:59 , LYS B:61 , ASN B:92 , ASP B:93 , GLY B:109 , ASP B:112 , SER B:130 , LYS B:159 , TPS B:2002 , MG B:2006 , HOH B:3022 , HOH B:3029 , HOH B:3057 , HOH B:3081 , HOH B:3149 , HOH B:3202BINDING SITE FOR RESIDUE POP B 2004
07MGAAUTHORASP A:93 , ASP A:112MG BINDING SITE
08MGBAUTHORASP B:93 , ASP B:112MG BINDING SITE
09PPAAUTHORARG A:59 , LYS A:61 , LYS A:159 , SER A:130 , ASN A:92PYROPHOSPHATE BINDING SITE
10PPBAUTHORARG B:59 , LYS B:61 , LYS B:159 , SER B:130 , ASN B:92PYROPHOSPHATE BINDING SITE
11TPAAUTHORTYR A:29 , HIS A:107 , TYR A:147 , ILE A:186 , ILE A:208 , GLN A:57 , THR A:156 , THR A:158 , GLY A:188 , SER A:209THIAMIN PHOSPHATE BINDING SITE
12TPBAUTHORTYR B:29 , HIS B:107 , TYR B:147 , ILE B:186 , ILE B:208 , GLN B:57 , THR B:156 , THR B:158 , GLY B:188 , SER B:209THIAMIN PHOSPHATE BINDING SITE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:151 -Pro A:152
2Gly B:151 -Pro B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2TPS)

(-) 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:226
 aligned with THIE_BACSU | P39594 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:226
                                1                                                                                                                                                                                                                             
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      
           THIE_BACSU     - ----MTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 222
               SCOP domains d2tpsa_ A: Thiamin phosphate synthase                                                                                                                                                                                              SCOP domains
               CATH domains 2tpsA00 A:10-235 Aldolase class I                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..eeeee.hhh....hhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh....eeee......hhhhhhhh...eeeeee..hhhhhhhhhh...eeee..................hhhhhhhh.....eeeee........hhhhh....eeee.hhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tps A  10 HGIRMTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229      


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with THIE_BACSU | P39594 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:227
                                 1                                                                                                                                                                                                                             
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
           THIE_BACSU     - -----MTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 222
               SCOP domains d2tpsb_ B: Thiamin phosphate synthase                                                                                                                                                                                               SCOP domains
               CATH domains 2tpsB00 B:9-235 Aldolase class I                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh..eeeee.hhh....hhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhh...eeee......hhhhhhh....eeeeee..hhhhhhhhhh...eeee..................hhhhhhhh.....eeeee....hhhhhhhhh....eeee.hhhh....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tps B   9 HHGIRMTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 235
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2TPS)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THIE_BACSU | P39594)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004789    thiamine-phosphate diphosphorylase activity    Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H(+) = diphosphate + thiamine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
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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        THIE_BACSU | P39594: 1g4e 1g4p 1g4s 1g4t 1g67 1g69 1g6c 3o15 3o16

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