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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi10 – 101Divalent metal cation
Metal bindingi12 – 121Divalent metal cation
Sitei36 – 361Transition state stabilizerUniRule annotation
Metal bindingi44 – 441Divalent metal cation
Binding sitei67 – 671Substrate; via carbonyl oxygenUniRule annotation
Sitei135 – 1351Transition state stabilizerUniRule annotation
Binding sitei144 – 1441SubstrateUniRule annotation

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

BioCyciBPSE320372:GBYB-2511-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1621622-C-methyl-D-erythritol 2,4-cyclodiphosphate synthasePRO_0000237710Add
BLAST

Interactioni

Subunit structurei

Homotrimer.UniRule annotation3 Publications

Chemistry

BindingDBiQ3JRA0.

Structurei

Secondary structure

1
162
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 1614Combined sources
Beta strandi20 – 223Combined sources
Beta strandi25 – 273Combined sources
Beta strandi30 – 334Combined sources
Beta strandi35 – 373Combined sources
Helixi41 – 5313Combined sources
Helixi59 – 624Combined sources
Helixi68 – 703Combined sources
Helixi75 – 8814Combined sources
Beta strandi91 – 10111Combined sources
Beta strandi103 – 1053Combined sources
Helixi108 – 1103Combined sources
Helixi111 – 12212Combined sources
Helixi126 – 1283Combined sources
Beta strandi129 – 1346Combined sources
Helixi140 – 1434Combined sources
Beta strandi146 – 15813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 4-158.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ3JRA0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 123Substrate binding
Regioni36 – 372Substrate bindingUniRule annotation
Regioni40 – 489Substrate binding
Regioni58 – 603Substrate binding
Regioni63 – 675Substrate binding
Regioni102 – 1087Substrate binding
Regioni133 – 1375Substrate binding

Sequence similaritiesi

Belongs to the IspF family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.
OrthoDBiEOG6J48RZ.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF.
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
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. Positions 4-158.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiQ3JRA0.

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.
OrthoDBiEOG6J48RZ.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.
BioCyciBPSE320372:GBYB-2511-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ3JRA0.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF.
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...

Publicationsi

« Hide 'large scale' publications
  1. Woods D.E., Nierman W.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1710b.
  2. "Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP."
    Seattle structural genomics center for infectious disease (SSGCID)
    Submitted (OCT-2008) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND ZINC IONS, COFACTOR, SUBUNIT.
  3. "Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with a fragment-nucleoside fusion D000161829."
    Seattle Structural Genomics Center for Infectious Disease (SSGCID)
    Edwards T.E., Davies D.R., Hartley R., Zeller W.
    Submitted (OCT-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND ZINC IONS, COFACTOR, SUBUNIT.
  4. "Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei."
    Begley D.W., Hartley R.C., Davies D.R., Edwards T.E., Leonard J.T., Abendroth J., Burris C.A., Bhandari J., Myler P.J., Staker B.L., Stewart L.J.
    J. Struct. Funct. Genomics 12:63-76(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND ZINC IONS, COFACTOR, SUBUNIT.

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 11, 2015
This is version 70 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.