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Protein

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Gene

ispF

Organism
Burkholderia pseudomallei (strain 1710b)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).UniRule annotation

Catalytic activityi

2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.UniRule annotation

Cofactori

a divalent metal cationUniRule annotation3 PublicationsNote: Binds 1 divalent metal cation per subunit.UniRule annotation3 Publications

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 4 of the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate.UniRule annotation
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)
  2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispD)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE)
  4. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF)
  5. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (ispG)
  6. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH)
This subpathway is part of the pathway isopentenyl diphosphate biosynthesis via DXP pathway, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate, the pathway isopentenyl diphosphate biosynthesis via DXP pathway and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi10Divalent metal cation1
Metal bindingi12Divalent metal cation1
Sitei36Transition state stabilizerUniRule annotation1
Metal bindingi44Divalent metal cation1
Binding sitei67Substrate; via carbonyl oxygenUniRule annotation1
Sitei135Transition state stabilizerUniRule annotation1
Binding sitei144SubstrateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.

Names & Taxonomyi

Protein namesi
Recommended name:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseUniRule annotation (EC:4.6.1.12UniRule annotation)
Short name:
MECDP-synthaseUniRule annotation
Short name:
MECPP-synthaseUniRule annotation
Short name:
MECPSUniRule annotation
Gene namesi
Name:ispFUniRule annotation
Ordered Locus Names:BURPS1710b_2511
OrganismiBurkholderia pseudomallei (strain 1710b)
Taxonomic identifieri320372 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
Proteomesi
  • UP000002700 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002377101 – 1622-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST162

Interactioni

Subunit structurei

Homotrimer.UniRule annotation3 Publications

Structurei

Secondary structure

1162
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 16Combined sources14
Beta strandi20 – 22Combined sources3
Beta strandi25 – 27Combined sources3
Beta strandi30 – 33Combined sources4
Beta strandi35 – 37Combined sources3
Helixi41 – 53Combined sources13
Helixi59 – 62Combined sources4
Helixi68 – 70Combined sources3
Helixi75 – 88Combined sources14
Beta strandi91 – 101Combined sources11
Beta strandi103 – 105Combined sources3
Helixi108 – 110Combined sources3
Helixi111 – 122Combined sources12
Helixi126 – 128Combined sources3
Beta strandi129 – 134Combined sources6
Helixi140 – 143Combined sources4
Beta strandi146 – 158Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3F0DX-ray1.20A/B/C/D/E/F1-162[»]
3F0EX-ray2.05A/B/C1-162[»]
3F0FX-ray2.09A/B/C1-162[»]
3F0GX-ray2.08A/B/C/D/E/F1-162[»]
3IEQX-ray2.10A/B/C1-162[»]
3JVHX-ray1.69A/B/C1-162[»]
3K14X-ray1.70A/B/C1-162[»]
3K2XX-ray1.85A/B/C1-162[»]
3KE1X-ray2.05A/B/C1-162[»]
3MBMX-ray1.80A/B/C1-162[»]
3P0ZX-ray1.95A/B/C1-162[»]
3P10X-ray1.70A/B/C1-162[»]
3QHDX-ray1.70A/B/C1-162[»]
ProteinModelPortaliQ3JRA0.
SMRiQ3JRA0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ3JRA0.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 12Substrate binding3
Regioni36 – 37Substrate bindingUniRule annotation2
Regioni40 – 48Substrate binding9
Regioni58 – 60Substrate binding3
Regioni63 – 67Substrate binding5
Regioni102 – 108Substrate binding7
Regioni133 – 137Substrate binding5

Sequence similaritiesi

Belongs to the IspF family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.

Family and domain databases

CDDicd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF. 1 hit.
InterProiIPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]
PfamiPF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00151. ispF. 1 hit.
PROSITEiPS01350. ISPF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q3JRA0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDFRIGQGYD VHQLVPGRPL IIGGVTIPYE RGLLGHSDAD VLLHAITDAL
60 70 80 90 100
FGAAALGDIG RHFSDTDPRF KGADSRALLR ECASRVAQAG FAIRNVDSTI
110 120 130 140 150
IAQAPKLAPH IDAMRANIAA DLDLPLDRVN VKAKTNEKLG YLGRGEGIEA
160
QAAALVVREA AA
Length:162
Mass (Da):17,175
Last modified:November 8, 2005 - v1
Checksum:i77F4A6B473C5961C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA47450.1.
RefSeqiWP_004191369.1. NC_007434.1.

Genome annotation databases

EnsemblBacteriaiABA47450; ABA47450; BURPS1710b_2511.
KEGGibpm:BURPS1710b_2511.
PATRICi19237514. VBIBurPse115837_2627.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA47450.1.
RefSeqiWP_004191369.1. NC_007434.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3F0DX-ray1.20A/B/C/D/E/F1-162[»]
3F0EX-ray2.05A/B/C1-162[»]
3F0FX-ray2.09A/B/C1-162[»]
3F0GX-ray2.08A/B/C/D/E/F1-162[»]
3IEQX-ray2.10A/B/C1-162[»]
3JVHX-ray1.69A/B/C1-162[»]
3K14X-ray1.70A/B/C1-162[»]
3K2XX-ray1.85A/B/C1-162[»]
3KE1X-ray2.05A/B/C1-162[»]
3MBMX-ray1.80A/B/C1-162[»]
3P0ZX-ray1.95A/B/C1-162[»]
3P10X-ray1.70A/B/C1-162[»]
3QHDX-ray1.70A/B/C1-162[»]
ProteinModelPortaliQ3JRA0.
SMRiQ3JRA0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA47450; ABA47450; BURPS1710b_2511.
KEGGibpm:BURPS1710b_2511.
PATRICi19237514. VBIBurPse115837_2627.

Phylogenomic databases

HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.

Miscellaneous databases

EvolutionaryTraceiQ3JRA0.

Family and domain databases

CDDicd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF. 1 hit.
InterProiIPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]
PfamiPF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00151. ispF. 1 hit.
PROSITEiPS01350. ISPF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiISPF_BURP1
AccessioniPrimary (citable) accession number: Q3JRA0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: November 8, 2005
Last modified: November 2, 2016
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.