1G4T - JenaLib

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Title :   THIAMIN PHOSPHATE SYNTHASE

Authors :   D. H. Peapus, H. -J. Chiu, N. Campobasso, J. J. Reddick, T. P. Begley, S. E. Ealick

Date :   28 Oct 00 (Deposition) - 26 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Thiamin Biosynthesis, Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Peapus, H. J. Chiu, N. Campobasso, J. J. Reddick, T. P. Begley, S. E. Ealick
Structural Characterization Of The Enzyme-Substrate, Enzyme-Intermediate, And Enzyme-Product Complexes Of Thiamin Phosphate Synthase.
Biochemistry V. 40 10103 2001
PubMed-ID: 11513589 | Reference-DOI: 10.1021/BI0104726
(for further references see the PDB file header)

Molecule 1 - THIAMIN PHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PYZC6927
	Expression System Strain	:	SG13009 WITH PREP4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	THIC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Other Details	:	COMPLEXED WITH TRIFLUORO-THIAMIN PHOSPHATE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FTP	2	Ligand/Ion	3-(4-AMINO-2-TRIFLUOROMETHYL-PYRIMIDIN-5-YLMETHYL)-4-METHYL-5-(2-PHOSPHONATOOXY-ETHYL)-THIAZOL-3-IUM
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FTP	1	Ligand/Ion	3-(4-AMINO-2-TRIFLUOROMETHYL-PYRIMIDIN-5-YLMETHYL)-4-METHYL-5-(2-PHOSPHONATOOXY-ETHYL)-THIAZOL-3-IUM
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FTP	1	Ligand/Ion	3-(4-AMINO-2-TRIFLUOROMETHYL-PYRIMIDIN-5-YLMETHYL)-4-METHYL-5-(2-PHOSPHONATOOXY-ETHYL)-THIAZOL-3-IUM
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:93 , ASP A:112 , POP A:2003 , HOH A:2101 , HOH A:2102	BINDING SITE FOR RESIDUE MG A 2005
2	AC2	SOFTWARE	ASP B:1093 , ASP B:1112 , POP B:2004 , HOH B:2201 , HOH B:2202	BINDING SITE FOR RESIDUE MG B 2006
3	AC3	SOFTWARE	TYR A:29 , ILE A:31 , GLN A:57 , ARG A:59 , ASN A:92 , HIS A:107 , SER A:130 , TYR A:147 , GLY A:149 , THR A:156 , THR A:158 , LYS A:159 , VAL A:184 , ILE A:186 , GLY A:188 , SER A:206 , MET A:207 , ILE A:208 , SER A:209 , POP A:2003 , HOH A:2301 , HOH A:2302 , HOH A:2305	BINDING SITE FOR RESIDUE FTP A 2001
4	AC4	SOFTWARE	TYR B:1029 , ILE B:1031 , GLN B:1057 , ARG B:1059 , ASN B:1092 , HIS B:1107 , SER B:1130 , TYR B:1147 , GLY B:1149 , THR B:1156 , THR B:1158 , LYS B:1159 , VAL B:1184 , ILE B:1186 , GLY B:1188 , SER B:1206 , MET B:1207 , ILE B:1208 , SER B:1209 , POP B:2004 , HOH B:2401 , HOH B:2402 , HOH B:2405	BINDING SITE FOR RESIDUE FTP B 2002
5	AC5	SOFTWARE	ARG A:59 , LYS A:61 , ASN A:92 , ASP A:93 , GLY A:109 , ASP A:112 , SER A:130 , LYS A:159 , FTP A:2001 , MG A:2005 , HOH A:2101 , HOH A:2102 , HOH A:2103 , HOH A:2104 , HOH A:2105 , HOH A:2107	BINDING SITE FOR RESIDUE POP A 2003
6	AC6	SOFTWARE	ARG B:1059 , LYS B:1061 , ASN B:1092 , ASP B:1093 , GLY B:1109 , ASP B:1112 , SER B:1130 , LYS B:1159 , FTP B:2002 , MG B:2006 , HOH B:2201 , HOH B:2202 , HOH B:2203 , HOH B:2204 , HOH B:2205 , HOH B:2207	BINDING SITE FOR RESIDUE POP B 2004

(no "SS Bond" information available for 1G4T)

Asymmetric Unit

No.	Residues
1	Gly A:151	-	Pro A:152
2	Gly B:1151	-	Pro B:1152

(no "SAP(SNP)/Variant" information available for 1G4T)

(no "PROSITE Motif" information available for 1G4T)

(no "Exon" information available for 1G4T)

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 d1g4ta_ A: Thiamin phosphate synthase                                                                                                                                                                                              SCOP domains
               CATH domains 1g4tA00 A:10-235 Aldolase class I                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh..eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee.................hhhhhhhhhh.....eeee.......hhhhhhh....eeehhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1g4t 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 d1g4tb_ B: Thiamin phosphate synthase                                                                                                                                                                                               SCOP domains
               CATH domains 1g4tB00 B:1009-1235 Aldolase class I                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh..eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee.................hhhhhhhhhh.....eeee.......hhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1g4t B 1009 HHGIRMTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 1235
                                  1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Thiamin phosphate synthase (12)

Family: Thiamin phosphate synthase (11)

Protein domain: Thiamin phosphate synthase (10)

Bacillus subtilis [TaxId: 1423] (9)

1a	d1g4ta_	A:
1b	d1g4tb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Bacillus subtilis. Organism_taxid: 1423. (10)

1a	1g4tB00	B:1009-1235
1b	1g4tA00	A:10-235

(no "Pfam Domain" information available for 1G4T)

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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	Cis Peptide Bonds
		Gly A:151 - Pro A:152	[ RasMol ]
		Gly B:1151 - Pro B:1152	[ RasMol ]

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	THIE_BACSU \| P39594	:	1g4e 1g4p 1g4s 1g67 1g69 1g6c 2tps 3o15 3o16

1g4e
1g4p
1g4s
1g67
1g69
1g6c
2tps	THIAMIN PHOSPHATE SYNTHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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