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(-) Description

Title :  CRYSTAL STRUCTURE OF THIAMIN PHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  K. M. Mcculloch, D. Ramamoorthy, K. Ishida, W. C. Guida, T. P. Begley, S.
Date :  28 Jul 10  (Deposition) - 27 Jul 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Thiamin Biosynthesis, Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Mcculloch, D. Ramamoorthy, K. Ishida, W. C. Guida, T. P. Begley, S. E. Ealick
Crystal Structure And Identification Of Potential Inhibitor Compounds For Mycobacterium Tuberculosis Thiamin Phosphate Synthase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THIAMINE-PHOSPHATE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28NTEV
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MT0427, MTCY22G10.11C, RV0414C, THIE
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: TMP PYROPHOSPHORYLASE, TMP-PPASE, THIAMINE-PHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:98 , GLN A:99 , ARG A:100 , HIS A:122BINDING SITE FOR RESIDUE PO4 A 223
2AC2SOFTWAREGLY B:98 , GLN B:99 , ARG B:100 , HIS B:122 , HOH B:261BINDING SITE FOR RESIDUE PO4 B 223

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O63)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:141 -Pro A:142
2Gly B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O63)

(-) Exons   (0, 0)

(no "Exon" information available for 3O63)

(-) 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:214
 aligned with THIE_MYCTO | P9WG74 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:222
                             1                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
           THIE_MYCTO     - -MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
               SCOP domains d3o63a_ A: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..eeee.....hhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee........-----..hhhhhhhhhh.---...eeee......hhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o63 A   0 HMHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPT-----APGLGLVRVAAEL---DKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        |-    |  159      |  -|      179       189       199       209       219  
                                                                                                                                                                              148   154         166 170                                                   


Chain A from PDB  Type:PROTEIN  Length:214
 aligned with THIE_MYCTU | P9WG75 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:222
                             1                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
           THIE_MYCTU     - -MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
               SCOP domains d3o63a_ A: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..eeee.....hhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee........-----..hhhhhhhhhh.---...eeee......hhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o63 A   0 HMHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPT-----APGLGLVRVAAEL---DKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        |-    |  159      |  -|      179       189       199       209       219  
                                                                                                                                                                              148   154         166 170                                                   


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with THIE_MYCTO | P9WG74 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           THIE_MYCTO     1 MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
               SCOP domains d3o63b_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhh...eeee.....hhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee.....--------..hhhhhhhhhh.---...eeee......hhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o63 B   1 MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWP--------APGLGLVRVAAEL---DKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    -   |   160     | 170       180       190       200       210       220 
                                                                                                                                                                          145      154         166 170                                                   


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with THIE_MYCTU | P9WG75 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           THIE_MYCTU     1 MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
               SCOP domains d3o63b_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.eeeee.......hhhhhhhhhhhh...eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhh...eeee.....hhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee.....--------..hhhhhhhhhh.---...eeee......hhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o63 B   1 MHESRLASARLYLCTDARRERGDLAQFAEAALAGGVDIIQLRDKGSPGELRFGPLQARDELAACEILADAAHRYGALFAVNDRADIARAAGADVLHLGQRDLPVNVARQILAPDTLIGRSTHDPDQVAAAAAGDADYFCVGPCWP--------APGLGLVRVAAEL---DKPWFAIGGINAQRLPAVLDAGARRIVVVRAITSADDPRAAAEQLRSALTAA 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    -   |   160     | 170       180       190       200       210       220 
                                                                                                                                                                          145      154         166 170
   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 3O63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O63)

(-) Gene Ontology  (8, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THIE_MYCTU | P9WG75)
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.

Chain A,B   (THIE_MYCTO | P9WG74)
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.

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  3o63
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  THIE_MYCTO | P9WG74
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  2.5.1.3
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3O63)

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