1OLY - JenaLib

Theoretical Model (Jmol Viewer)

Title :   HUMAN THIAMIN PYROPHOSPHOKINASE / PP20

Authors :   L. Barna, S. Bellyei, A. Szigeti, A. Boronkai, N. G. Than, P. Zavodszky, B. Sumegi

Date :   19 Aug 03 (Deposition) - 24 Sep 04 (Release) - 27 Jan 05 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B

Keywords :   Thiamin Pyrophosphokinase, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bellyei, A. Szigeti, A. Boronkai, Z. Szabo, J. Bene, T. Janaky, L. Barna, K. Sipos, O. Minik, A. Kravjak, R. Ohmacht, B. Melegh, P. Zavodszky, G. N. Than, B. Sumegi, H. Bohn, N. G. Than
Cloning, Sequencing, Structural And Molecular Biological Characterization Of Placental Protein 20 (Pp20)/Human Thiamin Pyrophosphokinase (Htpk)
Placenta V. 26 34 2005
PubMed: search
(for further references see the PDB file header)

Molecule 1 - THIAMIN PYROPHOSPHOKINASE
	Chains	:	A, B
	EC Number	:	2.7.6.2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	THIAMINE PYROPHOSPHOKINASE, THIAMINE DIPHOSPHOKINASE
	Tissue	:	PLACENTA


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 2)

No.	Name	Count	Type	Full Name
1	VIB	2	Ligand/Ion	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM

(no "Site" information available for 1OLY)

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

(no "Cis Peptide Bond" information available for 1OLY)

Theoretical Model (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)

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

Theoretical Model (8, 16)

	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	2	A:1-15 B:1-15	15 15
1.3	ENST00000360057	3	ENSE00001730714	chr7:144463044-144462973	72	TPK1_HUMAN	15-39	25	2	A:15-39 B:15-39	25 25
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 B:168-205	38 38
1.18c	ENST00000360057	18c	ENSE00001925028	chr7:144150756-144149034	1723	TPK1_HUMAN	205-243	39	2	A:205-243 B:205-243	39 39

Theoretical Model

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

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           TPK1_HUMAN     1 MEHAFTPLEPLLSTGNLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIKS 243
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhhhh.hhhhh...eeeehhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh...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 1.2       ----------------------------------------------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             -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.3  PDB: A:15-39   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18c  PDB: A:205-243              Transcript 1 (2)
           Transcript 1 (3) --------------------------------------Exon 1.7  PDB: A:39-62  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1oly A   1 MEHAFTPLEPLLSTGNLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIKS 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           TPK1_HUMAN     1 MEHAFTPLEPLLSTGNLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIKS 243
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhhhh.hhhhh...eeeehhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh...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 1.2       ----------------------------------------------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             -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.3  PDB: B:15-39   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18c  PDB: B:205-243              Transcript 1 (2)
           Transcript 1 (3) --------------------------------------Exon 1.7  PDB: B:39-62  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1oly B   1 MEHAFTPLEPLLSTGNLKYCLVILNQPLDNYFRHLWNKALLRACADGGANRLYDITEGERESFLPEFINGDFDSIRPEVREYYATKGCELISTPDQDHTDFTKCLKMLQKKIEEKDLKVDVIVTLGGLAGRFDQIMASVNTLFQATHITPFPIIIIQEESLIYLLQPGKHRLHVDTGMEGDWCGLIPVGQPCMQVTTTGLKWNLTNDVLAFGTLVSTSNTYDGSGVVTVETDHPLLWTMAIKS 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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 '\|'

(no "SCOP Domain" information available for 1OLY)

(no "CATH Domain" information available for 1OLY)

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

Theoretical Model(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.

Theoretical Model
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		VIB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1oly)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1oly)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Theoretical Model PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1oly
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TPK1_HUMAN \| Q9H3S4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.6.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	614458
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TPK1_HUMAN \| Q9H3S4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TPK1_HUMAN \| Q9H3S4	:	3s4y

(no "Related Entries Specified in the PDB File" available for 1OLY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (0, 0)

Exons (8, 16)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File