1HX3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF E.COLI ISOPENTENYL DIPHOSPHATE:DIMETHYLALLYL DIPHOSPHATE ISOMERASE

Authors :   V. Durbecq, G. Sainz, Y. Oudjama, B. Clantin, C. Bompard-Gilles, C. Tricot, J. Caillet, V. Stalon, L. Droogmans, V. Villeret

Date :   11 Jan 01 (Deposition) - 11 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Isopentenyl, Dimethylallyl, Isomerase, Isoprenoids (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Durbecq, G. Sainz, Y. Oudjama, B. Clantin, C. Bompard-Gilles, C. Tricot, J. Caillet, V. Stalon, L. Droogmans, V. Villeret
Crystal Structure Of Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase.
Embo J. V. 20 1530 2001
PubMed-ID: 11285217 | Reference-DOI: 10.1093/EMBOJ/20.7.1530
(for further references see the PDB file header)

Molecule 1 - ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PYL20
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET30B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DIMETHYLALLYL DIPHOSPHATE 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	LYS A:21 , ARG A:51 , ALA A:67 , HIS A:69 , IMD A:202 , HOH A:211 , HOH A:222	BINDING SITE FOR RESIDUE SO4 A 191
2	AC2	SOFTWARE	LYS B:21 , ARG B:51 , LYS B:55 , HIS B:69 , ARG B:83 , IMD B:203 , HOH B:219 , HOH B:241 , HOH B:264	BINDING SITE FOR RESIDUE SO4 B 191
3	AC3	SOFTWARE	HIS A:25 , HIS A:69	BINDING SITE FOR RESIDUE MN A 201
4	AC4	SOFTWARE	HIS B:25 , HIS B:69	BINDING SITE FOR RESIDUE MN B 202
5	AC5	SOFTWARE	ALA A:67 , HIS A:69 , TRP A:161 , SO4 A:191	BINDING SITE FOR RESIDUE IMD A 202
6	AC6	SOFTWARE	TRP B:161 , SO4 B:191	BINDING SITE FOR RESIDUE IMD B 203

(no "SS Bond" information available for 1HX3)

(no "Cis Peptide Bond" information available for 1HX3)

(no "SAP(SNP)/Variant" information available for 1HX3)

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 1HX3)

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: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 d1hx3a_ A: Isopentenyl diphosphate isomerase                                                                                                                                     SCOP domains
               CATH domains 1hx3A00 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...........eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx3 A   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVAGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 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 d1hx3b_ B: Isopentenyl diphosphate isomerase                                                                                                                                         SCOP domains
               CATH domains 1hx3B00 B:4-183 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........eee.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
                 1hx3 B   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVAGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLKL 183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

Legend:		→ Mismatch	(orange background)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d1hx3a_	A:
1b	d1hx3b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Homologous Superfamily: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Escherichia coli. Organism_taxid: 562. (11)

1a	1hx3A00	A:4-179
1b	1hx3B00	B:4-183

(no "Pfam Domain" information available for 1HX3)

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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1hzt	1HZT CONTAINS THE SAME PROTEIN(WILD TYPE).

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