1NFS - JenaLib

Title :   STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP

Authors :   J. Wouters

Date :   16 Dec 02 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

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

Keywords :   Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wouters, Y. Oudjama, S. J. Barkley, C. Tricot, V. Stalon, L. Droogmans, C. D. Poulter
Catalytic Mechanism Of Escherichia Coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, And Tyr-104 As Suggested By Crystal Structures Of Complexes With Transition State Analogues And Irreversible Inhibitors
J. Biol. Chem. V. 278 11903 2003
PubMed-ID: 12540835 | Reference-DOI: 10.1074/JBC.M212823200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:25 , HIS A:32 , HIS A:69 , GLU A:114 , GLU A:116	BINDING SITE FOR RESIDUE MN A 201
2	AC2	SOFTWARE	HIS B:25 , HIS B:32 , HIS B:69 , GLU B:114 , GLU B:116	BINDING SITE FOR RESIDUE MN B 201
3	AC3	SOFTWARE	CYS A:67 , GLU A:87 , DED A:301 , HOH A:508 , HOH A:509	BINDING SITE FOR RESIDUE MG A 401
4	AC4	SOFTWARE	CYS B:67 , GLU B:87 , DED B:302 , HOH B:522 , HOH B:523	BINDING SITE FOR RESIDUE MG B 401
5	AC5	SOFTWARE	LYS A:21 , ARG A:51 , LYS A:55 , CYS A:67 , GLY A:68 , HIS A:69 , ARG A:83 , GLU A:87 , TYR A:104 , GLU A:114 , GLU A:116 , TRP A:161 , MG A:401 , HOH A:506 , HOH A:508 , HOH A:509 , HOH A:512	BINDING SITE FOR RESIDUE DED A 301
6	AC6	SOFTWARE	LYS B:21 , ARG B:51 , LYS B:55 , CYS B:67 , GLY B:68 , HIS B:69 , ARG B:83 , GLU B:87 , TYR B:104 , GLU B:114 , GLU B:116 , MG B:401 , HOH B:516 , HOH B:523	BINDING SITE FOR RESIDUE DED B 302

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/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:176
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
            IDI_ECOLI     4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 179
               SCOP domains d1nfsa_ A: Isopentenyl diphosphate isomerase                                                                                                                                     SCOP domains
               CATH domains 1nfsA00 A:4-179 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........eee.eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nfs A   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:180
                                                                                                                                                                                                            182 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        |-
            IDI_ECOLI     4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLK-   -
               SCOP domains d1nfsb_ B: Isopentenyl diphosphate isomerase                                                                                                                                         SCOP domains
               CATH domains 1nfsB00 B:4-183 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------NUDIX-1nfsB01 B:31-165                                                                                                                 ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------NUDIX-1nfsB02 B:31-165                                                                                                                 ------------------ Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: B:30-164 UniProt: 30-164                                                                                                   ------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nfs B   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLKL 183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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 (1, 2)

Gene Ontology (8, 8)

Asymmetric/Biological 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/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
		DED	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1nfs
		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