_EC 5.3.3.2 Isopentenyl-diphosphate Delta-isomerase. 45 PDB entries  
EC 5.-.-.- Isomerases. [2,272 PDB entries]
EC 5.3.-.- Intramolecular oxidoreductases. [867 PDB entries]
EC 5.3.3.- Transposing C==C bonds. [220 PDB entries]
EC 5.3.3.2 Isopentenyl-diphosphate Delta-isomerase. [45 PDB entries]    
1hx3

Pathway: Terpenoid biosynthesis
Reaction: Isopentenyl diphosphate = dimethylallyl diphosphate.
 


Isopentenyl diphosphate
=
dimethylallyl diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Other name(s): Ipp isomerase. Isopentenylpyrophosphate Delta-isomerase. Isopentenylpyrophosphate isomerase. Methylbutenylpyrophosphate isomerase.
Cofactor(s): Fad or FMN; Mg(2+) or Ca(2+) or Mn(2+).
 

FAD
or
FMN
Mg(2+)
or Ca(2+)
or Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.
Links:   [IntEnz]   [ExPASy]   [KEGG]  

There are 45 PDB entries in enzyme class E.C.5.3.3.2

  PDB code Protein
1hx3
Crystal structure of e.Coli isopentenyl diphosphate:dimethylallyl diphosphate isomerase
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
1hzt
Crystal structure of metal-free isopentenyl diphosphate:dimethylallyl diphosphate isomerase
Source: Escherichia coli. Organism_taxid: 562. Gene: idi. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Chain: A (153 residues) CATH domain: 3.90.79.10
1i9a
Structural studies of cholesterol biosynthesis: mevalonate 5-diphosphate decarboxylase and isopentenyl diphosphate isomerase
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (178 residues) CATH domain: 3.90.79.10
1n2u
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase: complex with the bromohydrine of ipp
Source: Escherichia coli. Bacteria. Expressed in: escherichia coli.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group BHI is 87.00% similar to enzyme reactant Isopentenyl diphosphate
1nfs
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase: complex with nipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group DED is 64.00% similar to enzyme reactant Isopentenyl diphosphate
1nfz
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase: complex with eipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group EIP is 93.00% similar to enzyme reactant Isopentenyl diphosphate
1ow2
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase: complex of c67a mutant with eipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group EIP is 93.00% similar to enzyme reactant Isopentenyl diphosphate
1p0k
Ipp:dmapp isomerase type ii apo structure
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (306 residues) CATH domain: 3.20.20.70
1p0n
Ipp:dmapp isomerase type ii, fmn complex
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (305 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FMN corresponds to enzyme cofactor FMN
1ppv
Isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase in complex with the bromohydrine of ipp
Source: Escherichia coli. Organism_taxid: 562. Gene: idi or b2889. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group BHI is 93.00% similar to enzyme reactant Isopentenyl diphosphate
1ppw
Isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase in complex with the bromohydrine of ipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group EIP is 93.00% similar to enzyme reactant Isopentenyl diphosphate
1pvf
E.Coli ipp isomerase in complex with diphosphate
Source: Escherichia coli. Organism_taxid: 562. Gene: idi or b2889. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group DPO is 64.00% similar to enzyme reactant Isopentenyl diphosphate
1q54
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase: complex with the bromohydrine of ipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group BHI is 87.00% similar to enzyme reactant Isopentenyl diphosphate
1r67
Y104a mutant of e.Coli ipp isomerase
Source: Escherichia coli. Organism_taxid: 562. Gene: idi or b2889. Expressed in: escherichia coli. Expression_system_taxid: 562
Chain: A (151 residues) CATH domain: 3.90.79.10
1vcf
Crystal structure of ipp isomerase at i422
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (299 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FMN corresponds to enzyme cofactor FMN
1vcg
Crystal structure of ipp isomerase at p43212
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (311 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FMN corresponds to enzyme cofactor FMN
1x83
Y104f ipp isomerase reacted with (s)-bromohydrine of ipp
Source: Escherichia coli. Organism_taxid: 562. Gene: idi. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group SBH is 93.00% similar to enzyme reactant Isopentenyl diphosphate
1x84
Ipp isomerase (wt) reacted with (s)-bromohydrine of ipp
Source: Escherichia coli. Organism_taxid: 562. Gene: idi. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group SBH is 87.00% similar to enzyme reactant Isopentenyl diphosphate
2b2k
Structure of y104f idi-1 mutant in complex with eipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group EIP is 93.33% similar to enzyme reactant Isopentenyl
2dho
Crystal structure of human ipp isomerase i in space group p212121
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Chain: A (215 residues) CATH domain: Unassigned
2g73
Y104f mutant type 1 ipp isomerase complex with eipp
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group EIP is 93.00% similar to enzyme reactant Isopentenyl diphosphate
2g74
Y104f mutant of type 1 isopentenylpyrophosphate- dimethylallylpyrophosphate isomerase
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
2i6k
Crystal structure of human type i ipp isomerase complexed with a substrate analog
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chains: A, B (224 residues) CATH domain: Unassigned
Bound ligand:   Het Group EA2 is 73.00% similar to enzyme reactant Isopentenyl diphosphate
2icj
The crystal structure of human isopentenyl diphophate isomerase
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (219 residues) CATH domain: Unassigned
2ick
Human isopentenyl diphophate isomerase complexed with substrate analog
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (220 residues) CATH domain: Unassigned
Bound ligand:   Het Group DMA corresponds to enzyme reactant Isopentenyl diphosphate
2pny
Structure of human isopentenyl-diphosphate delta-isomerase 2
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: skeletal muscle. Gene: idi2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chain: A (233 residues) CATH domain: Unassigned
Bound ligand:   Het Group POP is 64.29% similar to enzyme reactant Isopentenyl
2veh
Monoclinic form of idi-1
Source: Expressed in: escherichia coli. Escherichia coli
Chains: A, B (176 residues) CATH domain: 3.90.79.10
2vej
Monoclinic form of idi-1
Source: Expressed in: escherichia coli. Escherichia coli
Chains: A, B (176 residues) CATH domain: 3.90.79.10
2vnp
Monoclinic form of idi-1
Source: Escherichia coli. Organism_taxid: 511693. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
Bound ligand:   Het Group DED is 64.00% similar to enzyme reactant Isopentenyl diphosphate
2vnq
Monoclinic form of idi-1
Source: Escherichia coli. Organism_taxid: 511693. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Chains: A, B (176 residues) CATH domain: 3.90.79.10
2zru
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with fmn
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (356 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FMN corresponds to enzyme cofactor FMN
2zrv
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with reduced fmn.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (361 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FNR corresponds to enzyme cofactor FMN
2zrw
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with fmn and ipp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group IPR corresponds to enzyme reactant Isopentenyl
  Het Group FMN corresponds to enzyme cofactor FMN
2zrx
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with fmn and dmapp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DMA corresponds to enzyme reactant Isopentenyl
  Het Group FMN corresponds to enzyme cofactor FMN
2zry
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with reduced fmn and ipp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group IPE corresponds to enzyme reactant Isopentenyl
  Het Group FNR corresponds to enzyme cofactor FMN
2zrz
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with reduced fmn and dmapp
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DMA corresponds to enzyme reactant Isopentenyl
  Het Group FNR corresponds to enzyme cofactor FMN
3b03
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with vipp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (363 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group VNR is 67.39% similar to enzyme cofactor FMN
3b04
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with oipp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (362 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group OOP is 65.96% similar to enzyme cofactor FMN
3b05
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with reduced fmn and ipp at 2.2a resol
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group IPE corresponds to enzyme reactant Isopentenyl
  Het Group FNR corresponds to enzyme cofactor FMN
3b06
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase in complex with reduced fmn and dmapp.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (364 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DMA corresponds to enzyme reactant Isopentenyl
  Het Group FNR corresponds to enzyme cofactor FMN
3dh7
Structure of t. Thermophilus idi-2 in complex with ppi
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Gene: tthb110. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B, C, D (318 residues) CATH domain: 3.20.20.70
3hyq
Crystal structure of isopentenyl-diphosphate delta-isomerase salmonella entericase
Source: Salmonella enterica subsp. Enterica se typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (151 residues) CATH domain: 3.90.79.10
3sr7
Crystal structure of s. Mutans isopentenyl pyrophosphate iso
Source: Streptococcus mutans. Organism_taxid: 1309. Strain: ua159. Gene: fni, smu_939. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (273 residues) CATH domain: 3.20.20.70
3vkj
Crystal structure of sulfolobus shibatae isopentenyl diphosp isomerase, octameric form
Source: Sulfolobus shibatae. Organism_taxid: 2286. Gene: fni, idi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (363 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group FNR corresponds to enzyme cofactor FMN
4n02
Type 2 idi from s. Pneumoniae
Source: Streptococcus pneumoniae. Organism_taxid: 516950. Strain: cgsp14
Chain: A (332 residues)
Bound ligand:   Het Group FNR corresponds to enzyme cofactor FMN