2VNQ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   MONOCLINIC FORM OF IDI-1

Authors :   J. De Ruyck, Y. Oudjama, J. Wouters

Date :   06 Feb 08 (Deposition) - 18 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Isoprene Biosynthesis, Polymorphism, Metal-Binding, Ipp Isomerase, Manganese, Cytoplasm, Isomerase, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. De Ruyck, Y. Oudjama, J. Wouters
Monoclinic Form Of Isopentenyl Diphosphate Isomerase: A Case Of Polymorphism In Biomolecular Crystals.
Acta Crystallogr. , Sect. F V. 64 239 2008
PubMed-ID: 18391416 | Reference-DOI: 10.1107/S174430910800568X

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511693
	Synonym	:	ISOPENTENYL DIPHOSPHATE ISOMERASE, IPP ISOMERASE,

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	IMD	2	Ligand/Ion	IMIDAZOLE
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	IMD	1	Ligand/Ion	IMIDAZOLE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	IMD	1	Ligand/Ion	IMIDAZOLE
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

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	ALA A:34 , CYS A:67 , GLY A:68 , HIS A:69 , TYR A:104 , GLU A:114 , GLU A:116 , TRP A:161 , SO4 A:401	BINDING SITE FOR RESIDUE IMD A 301
3	AC3	SOFTWARE	LYS A:21 , ARG A:51 , LYS A:55 , GLY A:68 , HIS A:69 , ARG A:83 , IMD A:301	BINDING SITE FOR RESIDUE SO4 A 401
4	AC4	SOFTWARE	HIS B:25 , HIS B:32 , HIS B:69 , GLU B:114 , GLU B:116	BINDING SITE FOR RESIDUE MN B 201
5	AC5	SOFTWARE	HIS B:69 , TYR B:104 , GLU B:114 , GLU B:116 , TRP B:161 , SO4 B:401	BINDING SITE FOR RESIDUE IMD B 301
6	AC6	SOFTWARE	LYS B:21 , ARG B:51 , LYS B:55 , HIS B:69 , ARG B:83 , IMD B:301 , HOH B:2039 , HOH B:2040	BINDING SITE FOR RESIDUE SO4 B 401

(no "SS Bond" information available for 2VNQ)

(no "Cis Peptide Bond" information available for 2VNQ)

(no "SAP(SNP)/Variant" information available for 2VNQ)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	IDI_ECOLI	30-164	2	A:30-164 B:30-164

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	IDI_ECOLI	30-164	1	A:30-164 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	IDI_ECOLI	30-164	1	- B:30-164

(no "Exon" information available for 2VNQ)

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: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 d2vnqa_ A: Isopentenyl diphosphate isomerase                                                                                                                                     SCOP domains
               CATH domains 2vnqA00 A:4-179 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vnq 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 d2vnqb_ B: Isopentenyl diphosphate isomerase                                                                                                                                         SCOP domains
               CATH domains 2vnqB00 B:4-183 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------NUDIX-2vnqB01 B:31-165                                                                                                                 ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------NUDIX-2vnqB02 B:31-165                                                                                                                 ------------------ Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: B:30-164 UniProt: 30-164                                                                                                   ------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vnq 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: IPP isomerase-like (23)

Protein domain: Isopentenyl diphosphate isomerase (16)

Escherichia coli [TaxId: 562] (15)

1a	d2vnqa_	A:
1b	d2vnqb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Homologous Superfamily: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Escherichia coli. Organism_taxid: 511693. (2)

1a	2vnqA00	A:4-179
1b	2vnqB00	B:4-183

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-2vnqB01	B:31-165
1b	NUDIX-2vnqB02	B:31-165

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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vnq)

Biological Units
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	2vnq
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	5.3.3.2
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1hx3	CRYSTAL STRUCTURE OF E.COLI ISOPENTENYLDIPHOSPHATE:DIMETHYLALLYL DIPHOSPHATE ISOMERASE
1hzt	CRYSTAL STRUCTURE OF METAL-FREE ISOPENTENYLDIPHOSPHATE:DIMETHYLALLYL DIPHOSPHATE ISOMERASE
1i9a	STRUCTURAL STUDIES OF CHOLESTEROL BIOSYNTHESIS : MEVALONATE5-DIPHOSPHATE DECARBOXYLASE AND ISOPENTENYL DIPHOSPHATEISOMERASE
1nfs	STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH NIPP
1nfz	STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH EIPP
1ow2	STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX OF C67A MUTANT WITH EIPP
1ppv	ISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP
1ppw	ISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE IN COMPLEX WITH THE BROMOHYDRINE OF IPP
1pvf	E.COLI IPP ISOMERASE IN COMPLEX WITH DIPHOSPHATE
1q54	STRUCTURE AND MECHANISM OF ACTION OFISOPENTENYLPYROPHOSPHATE- DIMETHYLALLYLPYROPHOSPHATEISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP
1r67	Y104A MUTANT OF E.COLI IPP ISOMERASE
1x83	Y104F IPP ISOMERASE REACTED WITH (S)- BROMOHYDRINE OF IPP
1x84	IPP ISOMERASE (WT) REACTED WITH (S)- BROMOHYDRINE OF IPP
2vnp	MONOCLINIC FORM OF IDI-1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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