2PNY - JenaLib

Title :   STRUCTURE OF HUMAN ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE 2

Authors :   J. R. Walker, T. Davis, C. Butler-Cole, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Struct Genomics Consortium (Sgc)

Date :   25 Apr 07 (Deposition) - 29 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym./Biol. Unit : A

Keywords :   Carotenoid Biosynthesis, Cholesterol Biosynthesis, Isomerase, Isoprene Biosynthesis, Lipid Synthesis, Peroxisome, Steroid Biosynthesis, Sterol Biosynthesis, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, T. Davis, C. Butler-Cole, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structure Of The Human Isopentenyl-Diphosphate Delta-Isomerase 2.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:86 , GLU A:115 , POP A:230 , HOH A:270 , HOH A:414	BINDING SITE FOR RESIDUE CA A 228
2	AC2	SOFTWARE	HIS A:40 , HIS A:51 , HIS A:88 , GLU A:146 , GLU A:148	BINDING SITE FOR RESIDUE MN A 229
3	AC3	SOFTWARE	ARG A:16 , LYS A:36 , ARG A:70 , LYS A:74 , THR A:76 , SER A:86 , SER A:87 , HIS A:88 , ARG A:111 , GLU A:115 , CA A:228 , HOH A:241 , HOH A:274 , HOH A:297 , HOH A:372 , HOH A:375	BINDING SITE FOR RESIDUE POP A 230
4	AC4	SOFTWARE	ARG A:203 , LYS A:223 , HIS A:225 , ARG A:226	BINDING SITE FOR RESIDUE GOL A 231
5	AC5	SOFTWARE	ARG A:-2 , ARG A:37 , LEU A:41 , GLU A:43 , GLN A:69 , LYS A:169 , HOH A:261 , HOH A:303	BINDING SITE FOR RESIDUE GOL A 232
6	AC6	SOFTWARE	HIS A:135 , ARG A:226 , VAL A:227 , HOH A:419	BINDING SITE FOR RESIDUE GOL A 233

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

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:233
 aligned with IDI2_HUMAN | Q9BXS1 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:233
                                  1                                                                                                                                                                                                                                  
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224   
           IDI2_HUMAN     - ------MSDINLDWVDRRQLQRLEEMLIVVDENDKVIGADTKRNCHLNENIEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYNPAELEEKDAIGVRRAAQRRLQAELGIPGEQISPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSQEELWELLEREARGEVKVTPWLRTIAERFLYRWWPHLDDVTPFVELHKIHRV 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------NUDIX-2pnyA01 A:50-200                                                                                                                                 --------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....hhhhhhhh..eeeee.....eeeeeehhhhhhhhhhh....eeeeeeeee.....eeeeee..............eee....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------NUDIX  PDB: A:49-199 UniProt: 49-199                                                                                                                   ---------------------------- PROSITE
           Transcript 1 (1) ------Exon 1.2  PDB: A:1-48 UniProt: 1-48             ------------------------------Exon 1.4  PDB: A:79-122 UniProt: 79-122     Exon 1.5  PDB: A:123-227 UniProt: 123-227                                                                 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.3  PDB: A:48-79          ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2pny A  -5 LVPRGSMSDINLDWVDRRQLQRLEEMLIVVDENDKVIGADTKRNCHLNENIEKGLLHRAFSVVLFNTKNRILIQQRSDTKVTFPGYFTDSCSSHPLYNPAELEEKDAIGVRRAAQRRLQAELGIPGEQISPEDIVFMTIYHHKAKSDRIWGEHEICYLLLVRKNVTLNPDPSETKSILYLSQEELWELLEREARGEVKVTPWLRTIAERFLYRWWPHLDDVTPFVELHKIHRV 227
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IDI2_HUMAN | Q9BXS1)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006695	cholesterol biosynthetic process	The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0050992	dimethylallyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
	GO:0046490	isopentenyl diphosphate metabolic process	The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
	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:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0016126	sterol biosynthetic process	The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
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.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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