1G67 - 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 :   03 Nov 00 (Deposition) - 26 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Other Details	:	COMPLEXED WITH 2-METHYL-5-METHYLENE-5H- PYRIMIDIN-4-YLIDENEAMINE, 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE AND PYROPHOSPHATE

		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 (4, 8)

No.	Name	Count	Type	Full Name
1	ICP	2	Ligand/Ion	2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-
4	TZP	2	Ligand/Ion	4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ICP	1	Ligand/Ion	2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-
4	TZP	1	Ligand/Ion	4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	ICP	1	Ligand/Ion	2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-
4	TZP	1	Ligand/Ion	4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE

Asymmetric Unit (8, 8)

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 2007
2	AC2	SOFTWARE	ASP B:1093 , ASP B:1112 , POP B:2004 , HOH B:2201 , HOH B:2202	BINDING SITE FOR RESIDUE MG B 2008
3	AC3	SOFTWARE	TYR A:29 , ILE A:31 , GLN A:57 , HIS A:107 , GLY A:149 , ILE A:186 , POP A:2003 , TZP A:2005	BINDING SITE FOR RESIDUE ICP A 2001
4	AC4	SOFTWARE	ARG A:59 , LYS A:61 , ASN A:92 , ASP A:93 , HIS A:107 , GLY A:109 , ASP A:112 , ALA A:130 , LYS A:159 , ICP A:2001 , TZP A:2005 , MG A:2007 , HOH A:2101 , HOH A:2102 , HOH A:2103 , HOH A:2105 , HOH A:2107	BINDING SITE FOR RESIDUE POP A 2003
5	AC5	SOFTWARE	ARG A:59 , THR A:156 , THR A:158 , LYS A:159 , ILE A:186 , GLY A:188 , MET A:207 , ILE A:208 , SER A:209 , ICP A:2001 , POP A:2003 , HOH A:2301 , HOH A:2302 , HOH A:2305	BINDING SITE FOR RESIDUE TZP A 2005
6	AC6	SOFTWARE	TYR B:1029 , ILE B:1031 , GLN B:1057 , HIS B:1107 , GLY B:1149 , POP B:2004 , TZP B:2006	BINDING SITE FOR RESIDUE ICP B 2002
7	AC7	SOFTWARE	ARG B:1059 , LYS B:1061 , ASN B:1092 , ASP B:1093 , GLY B:1109 , ASP B:1112 , ALA B:1130 , LYS B:1159 , ICP B:2002 , MG B:2008 , HOH B:2201 , HOH B:2202 , HOH B:2203 , HOH B:2205 , HOH B:2207 , HOH B:3200	BINDING SITE FOR RESIDUE POP B 2004
8	AC8	SOFTWARE	ARG B:1059 , THR B:1156 , THR B:1158 , LYS B:1159 , ILE B:1186 , GLY B:1188 , MET B:1207 , ILE B:1208 , SER B:1209 , ICP B:2002 , HOH B:2402 , HOH B:2405 , HOH B:3004	BINDING SITE FOR RESIDUE TZP B 2006

(no "SS Bond" information available for 1G67)

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 1G67)

(no "PROSITE Motif" information available for 1G67)

(no "Exon" information available for 1G67)

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:225
 aligned with THIE_BACSU | P39594 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:225
                               1                                                                                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
          THIE_BACSU      - ---MTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR  222
               SCOP domains d1g67a_ A: Thiamin phosphate synthase                                                                                                                                                                                             SCOP domains
               CATH domains 1g67A00 A:11-235 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...eeeehhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1g67 A   11 GIRMTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVAAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR  235
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with THIE_BACSU | P39594 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:225
                               1                                                                                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
          THIE_BACSU      - ---MTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR  222
               SCOP domains d1g67b_ B: Thiamin phosphate synthase                                                                                                                                                                                             SCOP domains
               CATH domains 1g67B00 B:1011-1235 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
                1g67 B 1011 GIRMTRISREMMKELLSVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGGDALTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVAAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRAVQGVSLIEAVRRQGISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREEIQTYKTGR 1235
                                  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d1g67a_	A:
1b	d1g67b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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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	1g67A00	A:11-235
1b	1g67B00	B:1011-1235

(no "Pfam Domain" information available for 1G67)

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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	1g67
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	THIE_BACSU \| P39594	:	1g4e 1g4p 1g4s 1g4t 1g69 1g6c 2tps 3o15 3o16

1g4e
1g4p
1g4s
1g4t
1g69
1g6c
2tps	THIAMIN PHOSPHATE SYNTHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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