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Title :   CRYSTAL STRUCTURE OF IPP ISOMERASE AT I422

Authors :   T. Wada, S. -Y. Park, R. H. Tame, S. Kuramitsu, S. Yokoyama, Riken Struc Genomics/Proteomics Initiative (Rsgi)

Date :   08 Mar 04 (Deposition) - 19 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A  (4x)
Biol. Unit 3: B  (4x)

Keywords :   Tim Barrel, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Wada, S. -Y. Park, R. H. Tame, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Ipp Isomerase At I422
To Be Published
PubMed: search

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (4x)	:	A
Biological Unit 3 (4x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	CD	1	Ligand/Ion	CADMIUM ION
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 48)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	FMN	8	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MSE	40	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 24)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 24)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:135 , ASP A:136 , ASP B:135	BINDING SITE FOR RESIDUE CD A 601
2	AC2	SOFTWARE	ALA A:65 , MSE A:66 , THR A:67 , GLY A:94 , SER A:95 , ASN A:123 , HIS A:152 , LYS A:187 , VAL A:189 , GLY A:190 , THR A:217 , TRP A:219 , GLY A:263 , GLY A:264 , TYR A:266 , ALA A:285 , ARG A:286	BINDING SITE FOR RESIDUE FMN A 501
3	AC3	SOFTWARE	ALA B:65 , MSE B:66 , THR B:67 , GLY B:94 , SER B:95 , ASN B:123 , HIS B:152 , LYS B:187 , VAL B:189 , GLY B:190 , THR B:217 , TRP B:219 , GLY B:263 , GLY B:264 , TYR B:266 , ALA B:285 , ARG B:286	BINDING SITE FOR RESIDUE FMN B 502

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

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

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

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

(no "Exon" information available for 1VCF)

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
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Chain A from PDB  Type:PROTEIN  Length:299
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:310
                                    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       322       332
           IDI2_THET2    23 KTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcfa1 A:23-332 Isopentenyl-diphosphate delt   a-isomerase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee........hhhhh...eee..eee...eee....---.hhhhhhhhhhhhhhhhh.eeeeeehhhhhhh..hhhhhh.........eeeeee.hhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhh.......hhhhhhhhhh.....eeee......hhhhhhhhh.....eee.......hhhhhhhh.--------.......hhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcf A  23 KTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmT---ENGERINLALAEAAEALGVGmmLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWV--------ELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    32        42        52        62   ||   72        82        92       102       112       122       132       142|      152       162       172       182  |    192       202       212       222   |     -  |    242       252       262       272       282       292       302       312       322       332
                                                                      66-MSE1                  91-MSE                                             143-MSE                                   185-MSE                                  226      235                                                                                                 
                                                                       67                       92-MSE

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with IDI2_THET2 | Q746I8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:310
                                    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       322       332
           IDI2_THET2    23 KTTTGLEGFRLRYQALAGLALGEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEALEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVMVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGAKNPKEARGRVERV 332
               SCOP domains d1vcfb_ B: Isopentenyl-diphosphate delta-isomerase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee........hhhhh...eee..eee...eee........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhh..hhhhhh.........eeeeee.hhhhh.hhhhhhhhhhhhh..eeeee.hhhhhhhh.......hhhhhhhhhh.....eeee......hhhhhhhhh.....eee............------------.......hhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcf B  23 KTTTGLEGFRLRYQALAGLALSEVDLTTPFLGKTLKAPFLIGAmTGGEENGERINLALAEAAEALGVGmmLGSGRILLERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEmLEADALAFHVNPLQEAVQRGDTDFRGLVERLAELLPLPFPVmVKEVGHGLSREAALALRDLPLAAVDVAGAGGTSWARV------------ELCEIGIPTARAILEVREVLPHLPLVASGGVYTGTDGAKALALGADLLAVARPLLRPALEGAERVAAWIGDYLEELRTALFAIGARNPKEARGRVERV 332
                                    32        42        52        62   |    72        82        92       102       112       122       132       142|      152       162       172       182  |    192       202       212       222         -  |    242       252       262       272       282       292       302       312       322       332
                                                                      66-MSE                   91-MSE                                             143-MSE                                   185-MSE                              222          235                                                                                                 
                                                                                                92-MSE

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: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: Isopentenyl-diphosphate delta-isomerase (4)

Thermus thermophilus [TaxId: 274] (1)

1a	d1vcfa1	A:23-332
1b	d1vcfb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (IDI2_THET2 | Q746I8)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0070402	NADPH binding	Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0004452	isopentenyl-diphosphate delta-isomerase activity	Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
	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: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:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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	IDI2_THET2 \| Q746I8	:	1vcg

1p0k
1p0n
1vcg	THE SAME PROTEIN AT P43212 RELATED ID: TTK003001255 RELATED DB: TARGETDB

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