1IG0 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST THIAMIN PYROPHOSPHOKINASE

Authors :   L. -J. Baker, J. A. Dorocke, R. A. Harris, D. E. Timm

Date :   16 Apr 01 (Deposition) - 20 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Substrate Complex, Compound Active Site, Alpha-Beta- Alpha, Beta Sandwich, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. Baker, J. A. Dorocke, R. A. Harris, D. E. Timm
The Crystal Structure Of Yeast Thiamin Pyrophosphokinase.
Structure V. 9 539 2001
PubMed-ID: 11435118 | Reference-DOI: 10.1016/S0969-2126(01)00615-3
(for further references see the PDB file header)

Molecule 1 - THIAMIN PYROPHOSPHOKINASE
	Chains	:	A, B
	EC Number	:	2.7.6.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	THI80
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:270 , VAL A:272 , SER A:285 , SER A:286 , SER A:287 , ASN A:288 , GLN B:122 , TYR B:123 , SER B:124 , THR B:125 , HOH B:805 , HOH B:971	BINDING SITE FOR RESIDUE VIB B 701
2	AC2	SOFTWARE	GLN A:122 , TYR A:123 , SER A:124 , THR A:125 , HOH A:784 , HOH A:1011 , TRP B:270 , VAL B:272 , SER B:285 , SER B:286 , SER B:287 , ASN B:288	BINDING SITE FOR RESIDUE VIB A 702

(no "SS Bond" information available for 1IG0)

(no "Cis Peptide Bond" information available for 1IG0)

(no "SAP(SNP)/Variant" information available for 1IG0)

(no "PROSITE Motif" information available for 1IG0)

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOR143C	1	YOR143C.1	XV:602343-601384	960	THI80_YEAST	1-319	319	2	A:3-319 B:1-319	317 319

Asymmetric/Biological 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:317
 aligned with THI80_YEAST | P35202 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       
          THI80_YEAST     3 EECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKIDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKYLPNYIIGDLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLISNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFDQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCFIDTKDDIILNVEIFVDKLIDFL 319
               SCOP domains d1ig0a2 A:3-223 Thiamin pyrophosphokinase, catalytic domain                                                                                                                                                                  d1ig0a1 A:224-319 Thiamin pyrophosphokinase, substrate-binding domain                            SCOP domains
               CATH domains 1ig0A02 A:3-36,A:224-319          1ig0A01 A:37-223 Thiamin pyrophosphokinase, domain 1                                                                                                                                       1ig0A02 A:3-36,A:224-319  [code=2.60.120.320, no name defined]                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...............eeee.hhhh......eeeeee.......hhhhhhhhhhhh.eeeee.hhhhhhhhhh..hhhhhh.....eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhh..hhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee...eeeeee....eeee.hhhhhhhheeeeeee.....eeeeeee...eeeeeeee.......eeee......eeeeee...eeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-319 UniProt: 1-319 [INCOMPLETE]                                                                                                                                                                                                                                                                            Transcript 1
                 1ig0 A   3 EECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKIDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKYLPNYIIGDLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLISNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFDQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCFIDTKDDIILNVEIFVDKLIDFL 319
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with THI80_YEAST | P35202 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
          THI80_YEAST     1 MSEECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKIDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKYLPNYIIGDLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLISNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFDQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCFIDTKDDIILNVEIFVDKLIDFL 319
               SCOP domains d1ig0b2 B:1-223 Thiamin pyrophosphokinase, catalytic domain                                                                                                                                                                    d1ig0b1 B:224-319 Thiamin pyrophosphokinase, substrate-binding domain                            SCOP domains
               CATH domains --1ig0B02 B:3-36,B:224-319          1ig0B01 B:37-223 Thiamin pyrophosphokinase, domain 1                                                                                                                                       1ig0B02 B:3-36,B:224-319  [code=2.60.120.320, no name defined]                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...............eeee.hhhh......eeeeee.......hhhhhhhhhhhh.eeeee.hhhhhhhhhh..hhhhhhhh...eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee...eeeeee....eeee.hhhhhhhheeeeeee.....eeeeeee...eeeeeeee.......eeee......eeeeee...eeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-319 UniProt: 1-319                                                                                                                                                                                                                                                                                           Transcript 1
                 1ig0 B   1 MSEECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKIDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKYLPNYIIGDLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLISNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFDQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCFIDTKDDIILNVEIFVDKLIDFL 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Thiamin pyrophosphokinase, domain 1 (5)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	1ig0A01	A:37-223
1b	1ig0B01	B:37-223

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.320, no name defined] (3)

Baker's yeast (Saccharomyces cerevisiae) (1)

2a	1ig0A02	A:3-36,A:224-319
2b	1ig0B02	B:3-36,B:224-319

(no "Pfam Domain" information available for 1IG0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (THI80_YEAST | P35202)

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.

Asymmetric/Biological Unit
	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
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ig0)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1ig0
		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
	THI80_YEAST \| P35202
		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)
	(no 'MIM ID' available)
		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
	THI80_YEAST \| P35202
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1IG0)

(no "Related Entries Specified in the PDB File" available for 1IG0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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