1I9A - JenaLib

Title :   STRUCTURAL STUDIES OF CHOLESTEROL BIOSYNTHESIS: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AND ISOPENTENYL DIPHOSPHATE ISOMERASE

Authors :   J. B. Bonanno, C. Edo, N. Eswar, U. Pieper, M. J. Romanowski, V. Ilyin, S. E. Gerchman, H. Kycia, F. W. Studier, A. Sali, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   18 Mar 01 (Deposition) - 28 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha/Beta Protein, Isomerase, Mn2+, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Bonanno, C. Edo, N. Eswar, U. Pieper, M. J. Romanowski, V. Ilyin, S. E. Gerchman, H. Kycia, F. W. Studier, A. Sali, S. K. Burley
Structural Genomics Of Enzymes Involved In Sterol/Isoprenoid Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 98 12896 2001
PubMed-ID: 11698677 | Reference-DOI: 10.1073/PNAS.181466998
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:178
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:178
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        
           IDI_ECOLI      4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQL  181
               SCOP domains d1i9aa_ A: Isopentenyl diphosphate isomerase                                                                                                                                       SCOP domains
               CATH domains 1i9aA00 A:4-181 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........eee.eee......hhhhhhhhhhhhhh.......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   ----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1i9a A    4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVmDYQWCDLADVLHGIDATPWAFSPWmVmQATNREARKRLSAFTQL  181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133   |   143       153       163|      173        
                                                                                                                                                               137-MSE                  162-MSE               
                                                                                                                                                                                          164-MSE

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:178
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        
           IDI_ECOLI      4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQL  181
               SCOP domains d1i9ab_ B: Isopentenyl diphosphate isomerase                                                                                                                                       SCOP domains
               CATH domains 1i9aB00 B:1004-1181 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.........................................hhhhhhhhhhhhhhh.............eeeee.....eeeee.........................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: B:1030-1164 UniProt: 30-164                                                                                                ----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1i9a B 1004 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVmDYQWCDLADVLHGIDATPWAFSPWmVmQATNREARKRLSAFTQL 1181
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133   |  1143      1153      1163|     1173        
                                                                                                                                                              1137-MSE                 1162-MSE               
                                                                                                                                                                                         1164-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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (IDI_ECOLI | Q46822)

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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0050992	dimethylallyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Visualization

Interactive Views

Asymmetric 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
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1i9a)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1i9a
		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
	IDI_ECOLI \| Q46822
		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)
	5.3.3.2
		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

Description