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Title :   CRYSTAL STRUCTURE OF HUMAN THIAMIN PYROPHOSPHOKINASE 1

Authors :   L. Shen, W. Tempel, Y. Tong, Y. Li, J. R. Walker, C. H. Arrowsmith, A. M. Ed C. Bountra, J. Weigelt, H. Park, Structural Genomics Consortium (

Date :   20 May 11 (Deposition) - 08 Jun 11 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Kinase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Shen, W. Tempel, Y. Tong, Y. Li, J. R. Walker, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Crystal Structure Of Human Thiamin Pyrophosphokinase 1
To Be Published
PubMed: search

Molecule 1 - THIAMIN PYROPHOSPHOKINASE 1
	Chains	:	A, B
	EC Number	:	2.7.6.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21-V2R-PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HTPK1, PLACENTAL PROTEIN 20, PP20, THIAMINE PYROPHOSPHOKINASE 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	SO4	5	Ligand/Ion	SULFATE ION
3	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE
4	UNX	9	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (3, 32)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	10	Ligand/Ion	SULFATE ION
3	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE
4	UNX	18	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:71 , ASP A:73 , GLN A:96 , ASP A:97 , HIS A:98 , THR A:99 , ASP A:100 , ARG A:131 , GLN A:134 , HOH A:327 , SO4 A:1302 , CA A:1303 , TRP B:202 , SER B:216 , THR B:217 , SER B:218 , ASN B:219	BINDING SITE FOR RESIDUE TPP A 1301
2	AC2	SOFTWARE	ASN A:25 , ALA A:45 , ASP A:46 , GLY A:47 , ASP A:73 , SER A:74 , ASP A:100 , GLN A:134 , HOH A:308 , HOH A:317 , TPP A:1301 , CA A:1303	BINDING SITE FOR RESIDUE SO4 A 1302
3	AC3	SOFTWARE	ASP A:46 , ASP A:71 , ASP A:73 , ASP A:100 , TPP A:1301 , SO4 A:1302	BINDING SITE FOR RESIDUE CA A 1303
4	AC4	SOFTWARE	TRP A:202 , SER A:216 , THR A:217 , SER A:218 , ASN A:219 , ASP B:71 , ASP B:73 , GLN B:96 , ASP B:97 , HIS B:98 , THR B:99 , ASP B:100 , ARG B:131 , GLN B:134 , HOH B:347 , HOH B:362 , SO4 B:1302 , CA B:1303	BINDING SITE FOR RESIDUE TPP B 1301
5	AC5	SOFTWARE	ASN B:25 , ASP B:46 , GLY B:47 , ASP B:73 , SER B:74 , ASP B:100 , HOH B:339 , TPP B:1301 , CA B:1303	BINDING SITE FOR RESIDUE SO4 B 1302
6	AC6	SOFTWARE	ASP B:46 , ASP B:71 , ASP B:73 , ASP B:100 , TPP B:1301 , SO4 B:1302	BINDING SITE FOR RESIDUE CA B 1303
7	AC7	SOFTWARE	GLY A:58 , GLU A:59 , ARG A:60 , HOH A:384 , HOH A:385 , HOH A:386 , HIS B:34	BINDING SITE FOR RESIDUE SO4 A 244
8	AC8	SOFTWARE	HIS A:34 , GLY B:58 , GLU B:59 , ARG B:60 , HOH B:297 , HOH B:299 , HOH B:320	BINDING SITE FOR RESIDUE SO4 B 244
9	AC9	SOFTWARE	HOH A:387 , HIS B:34 , ASN B:37 , HOH B:351	BINDING SITE FOR RESIDUE SO4 B 245

(no "SS Bond" information available for 3S4Y)

(no "Cis Peptide Bond" information available for 3S4Y)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_067391	L	40	P	TPK1_HUMAN	Disease (THMD5)	387906936	A/B	L	40	P
2	UniProt	VAR_067392	N	50	H	TPK1_HUMAN	Disease (THMD5)	387906935	A/B	N	50	H
3	UniProt	VAR_067393	N	219	S	TPK1_HUMAN	Disease (THMD5)	371271054	A/B	N	219	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_067391	L	40	P	TPK1_HUMAN	Disease (THMD5)	387906936	A/B	L	40	P
2	UniProt	VAR_067392	N	50	H	TPK1_HUMAN	Disease (THMD5)	387906935	A/B	N	50	H
3	UniProt	VAR_067393	N	219	S	TPK1_HUMAN	Disease (THMD5)	371271054	A/B	N	219	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3S4Y)

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000360057	1	ENSE00001409274	chr7:144533146-144533060	87	TPK1_HUMAN	-	0	0	-	-
1.2	ENST00000360057	2	ENSE00002182942	chr7:144532711-144532653	59	TPK1_HUMAN	1-15	15	0	-	-
1.3	ENST00000360057	3	ENSE00001730714	chr7:144463044-144462973	72	TPK1_HUMAN	15-39	25	2	A:16-39 B:16-39	24 24
1.7	ENST00000360057	7	ENSE00001770717	chr7:144380071-144380002	70	TPK1_HUMAN	39-62	24	2	A:39-62 B:39-62	24 24
1.10	ENST00000360057	10	ENSE00001726205	chr7:144345972-144345900	73	TPK1_HUMAN	62-86	25	2	A:62-86 B:62-86	25 25
1.13a	ENST00000360057	13a	ENSE00001598131	chr7:144320354-144320259	96	TPK1_HUMAN	87-118	32	2	A:87-118 B:87-118	32 32
1.15	ENST00000360057	15	ENSE00001793151	chr7:144288662-144288516	147	TPK1_HUMAN	119-167	49	2	A:119-167 B:119-167	49 49
1.16	ENST00000360057	16	ENSE00001748218	chr7:144245695-144245584	112	TPK1_HUMAN	168-205	38	2	A:168-205 (gaps) B:168-205 (gaps)	38 38
1.18c	ENST00000360057	18c	ENSE00001925028	chr7:144150756-144149034	1723	TPK1_HUMAN	205-243	39	2	A:205-242 B:205-242	38 38

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:224
 aligned with TPK1_HUMAN | Q9H3S4 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:227
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       
           TPK1_HUMAN    16 NLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIK 242
               SCOP domains d3s4ya1 A:16-158 Thiamin pyrophosphokinase, catalytic domain                                                                                   d3s4ya2 A:159-24   2 Thiamin pyrophosphokinase, substrate-binding domain             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhh..eeee.hhhhhhhhhh..hhhhh...eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeee.---.eeeeeeee.....eeeeeee........eee......eeee......eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------P---------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:16-39  ----------------------Exon 1.10  PDB: A:62-86  Exon 1.13a  PDB: A:87-118       Exon 1.15  PDB: A:119-167 UniProt: 119-167       Exon 1.16  PDB: A:168-205 (gaps)      ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.7  PDB: A:39-62  ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18c  PDB: A:205-242             Transcript 1 (2)
                 3s4y A  16 NLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHV---MEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIK 242
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165        |-  |    185       195       205       215       225       235       
                                                                                                                                                                                        174 178

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with TPK1_HUMAN | Q9H3S4 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:227
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       
           TPK1_HUMAN    16 NLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIK 242
               SCOP domains d3s4yb1 B:16-158 Thiamin pyrophosphokinase, catalytic domain                                                                                   d3s4yb2 B:159-24   2 Thiamin pyrophosphokinase, substrate-binding domain             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------TPK_catalytic-3s4yB03 B:25-158                                                                                                        ---------TPK_B1_   binding-3s4yB01 B:168-235                                 ------- Pfam domains (1)
           Pfam domains (2) ---------TPK_catalytic-3s4yB04 B:25-158                                                                                                        ---------TPK_B1_   binding-3s4yB02 B:168-235                                 ------- Pfam domains (2)
         Sec.struct. author ...eeeee.......hhhhhhhhh..eeee.hhhhhhhhhh..hhhhh...eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh......eeeee..eeeeee..eeeeee.---.eeeeeeee.....eeeeeee........eee......eeee......eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------P---------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:16-39  ----------------------Exon 1.10  PDB: B:62-86  Exon 1.13a  PDB: B:87-118       Exon 1.15  PDB: B:119-167 UniProt: 119-167       Exon 1.16  PDB: B:168-205 (gaps)      ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.7  PDB: B:39-62  ----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18c  PDB: B:205-242             Transcript 1 (2)
                 3s4y B  16 NLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHV---MEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIK 242
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165        |-  |    185       195       205       215       225       235       
                                                                                                                                                                                        174 178

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "CATH Domain" information available for 3S4Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TPK1_HUMAN | Q9H3S4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0030975	thiamine binding	Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0004788	thiamine diphosphokinase activity	Catalysis of the reaction: ATP + thiamine = AMP + thiamine diphosphate.
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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.
	GO:0006772	thiamine metabolic process	The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0042723	thiamine-containing compound metabolic process	The chemical reactions and pathways involving thiamine (vitamin B1), and compounds derived from it.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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(no "Related Entries Specified in the PDB File" available for 3S4Y)

Description

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Ligands, Modified Residues, Ions (4, 18)

Sites (9, 9)

SS Bonds (0, 0)

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