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Seattle Structural Genomics Center for Infectious Disease

BupsA.00122.a: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF)

Target Characteristics

from organism: Burkholderia pseudomallei 1710b
most recent status: in PDB
center reference id: BupsA.00122.a
is community request: True
associated disease: Melioidosis
NIH risk group: 3
is select agent: True
NIH priority
pathogens category:
IIIB

Ordering Clones & Proteins

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Proteins

CENTER
REFERENCE ID
DOMAIN/REGION
DESCRIPTION
INFO AA
START
AA
STOP
ORDER
MATERIAL
BupsA.00122.a.A1.PS00036 Full length( BupsA.00122.a ) 1 162

Structures

image of structure for 3F0D
3F0D
Deposited: 10/24/2008
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3F0E
3F0E
Deposited: 10/24/2008
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3F0F
3F0F
Deposited: 10/24/2008
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3F0G
3F0G
Deposited: 10/24/2008
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3IEQ
3IEQ
Deposited: 7/23/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3IEW
3IEW
Deposited: 7/23/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3IKE
3IKE
Deposited: 8/5/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3IKF
3IKF
Deposited: 8/5/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3JVH
3JVH
Deposited: 9/16/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3K14
3K14
Deposited: 9/25/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3K2X
3K2X
Deposited: 9/30/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3KE1
3KE1
Deposited: 10/23/2009
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3MBM
3MBM
Deposited: 3/25/2010
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PS00036
image of structure for 3P0Z
3P0Z
Deposited: 9/29/2010
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW29971
image of structure for 3P10
3P10
Deposited: 9/29/2010
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW29971
image of structure for 3Q8H
3Q8H
Deposited: 1/6/2011
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW29971
image of structure for 3QHD
3QHD
Deposited: 1/25/2011
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW29971
image of structure for 6MWF
6MWF
Deposited: 10/29/2018
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW28612
image of structure for 6MWI
6MWI
Deposited: 10/29/2018
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW28612
image of structure for 6MWJ
6MWJ
Deposited: 10/29/2018
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW28612
image of structure for 6MWK
6MWK
Deposited: 10/29/2018
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.A1.GE25234
Protein: BupsA.00122.a.A1.PW28612
image of structure for 6NMO
6NMO
Deposited: 1/11/2019
Determination: XRay
Diffraction Image
Clone: BupsA.00122.a.D11.GE00453
Protein: BupsA.00122.a.D11.PD00455

Publications by SSGCID

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Abendroth J, Begley DW, Bhandari J, Burris CA, Davies DR, Edwards TE, Hartley RC, Leonard JT, Myler PJ, Staker BL, Stewart LJ
J. Struct. Funct. Genomics - 2011
volume 12, issue 2, pages 63-76
PMID: 21359640; PMCID: PMC3123455
Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.
Begley DW, Blain J, Clare M, Edwards TE, Gogol K, Hagen TJ, Hartley RC, Horn JR, Jakkaraju S, Karlsson CA, Myler PJ, Staker BL, Stewart LJ, Zhang Z, Zhao L
Bioorg. Med. Chem. Lett. - 2013
volume 23, issue 24, pages 6860-3
PMID: 24157367; PMCID: PMC3874807
PDB: 3KE1, 3Q8H
Combining functional and structural genomics to sample the essential Burkholderia structome.
Abendroth J, Armour B, Barrett L, Baugh L, Begley DW, Buchko GW, Choi R, Clifton MC, Dieterich SH, Dranow DM, Edwards TE, Fairman JW, Fox D, Gallagher LA, Gardberg AS, Gillespie A, Manoil C, Myler PJ, Nakazawa-Hewitt S, Napuli A, Nguyen MT, Patrapuvich R, Phan I, Stacy R, Staker BL, Stewart LJ, Van Voorhis WC
PLoS ONE - 2012
volume 8, issue 1, pages e53851
PMID: 23382856; PMCID: PMC3561365

Citations by Others

Rare Sidechain Conformations in Proteins and DNA
BJ Hintze - 2015 - search.proquest.com
PDB: 3F0D
Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment
J Kalinowska-T, PK Fyfe, A Dawson and WN Hunter - BMC Structural Biology, 2014 - biomedcentral.com
PDB: 3F0G
Synthesis and Computational Analysis of Novel IspF Inhibitors
D Harper, M Rouffet, L Votapka- Bulletin of the American, 2018 - pointloma.whdl.org
PDB: 3IEW
Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function
P Chaskar, V Zoete, UF Röhrig - Journal of chemical information …, 2014 - ACS Publications
cited by: 11 others
PDB: 3IKF, 3JVH, 3K14, 3KE1
An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs
I Giangreco, DA Cosgrove? - Journal of chemical information and modeling, 2013 - ACS Publications
cited by: 4 others
PDB: 3K14
Molecular Recognition in Chemical and Biological Systems
E Persch, O Dumele, F Diederich - … Chemie International Edition, 2015 - Wiley Online Library
cited by: 148 others
PDB: 3KE1, 3Q8H
Molekulare Erkennung in chemischen und biologischen Systemen
E Persch, O Dumele, F Diederich - Angewandte Chemie, 2015 - Wiley Online Library
cited by: 21 others
PDB: 3KE1, 3Q8H
Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide
C Sch?rfer, T Schulz-Gasch, HC Ehrlich? - Journal of medicinal ?, 2013 - ACS Publications
cited by: 2 others
PDB: 3KE1
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX
JA Bell, KL Ho, R Farid - Acta Crystallographica Section D: Biological Crystallography, 2012 - scripts.iucr.org
cited by: 10 others
PDB: 3P10
Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI
R Rose, M Rose, C Ottmann - Journal of Structural Biology, 2012 - Elsevier
cited by: 6 others
PDB: 3P10
Development of Inhibitors of the 2 C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents
T Masini, AKH Hirsch - Journal of medicinal chemistry, 2014 - ACS Publications
cited by: 7 others
PDB: 3Q8H

This list was obtained from Google Scholar searches using the Open Source tool https://github.com/ckreibich/scholar.py and each citation has been manually reviewed.

External Resources

Resource Reference ID
OrthoMCL: OG5_130616
PATRIC ID: fig|320372.6.peg.2627
RefSeq: YP_333903
UniProt: Q3JRA0

Enzyme & Pathway Information

Pathway Pathway ID EC Number
methylerythritol phosphate pathway I NONMEVIPP-PWY 4.6.1.12
superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) PWY-5121 4.6.1.12
isoprene biosynthesis I PWY-6270 4.6.1.12
superpathway of ergosterol biosynthesis II PWY-7156 4.6.1.12
taxadiene biosynthesis (engineered) PWY-7392 4.6.1.12
methylerythritol phosphate pathway II PWY-7560 4.6.1.12

Sequences

These sequences are the native gene sequence; sequences of constructs derived from these sequences may differ due to codon optimization or other protocols. To find the specific sequence of any material you may have ordered, click on the "more" button next to the name of that material.
AA Sequence
MDFRIGQGYD VHQLVPGRPL IIGGVTIPYE RGLLGHSDAD VLLHAITDAL FGAAALGDIG RHFSDTDPRF KGADSRALLR ECASRVAQAG FAIRNVDSTI IAQAPKLAPH IDAMRANIAA DLDLPLDRVN VKAKTNEKLG YLGRGEGIEA QAAALVVREA AA

NT Sequence
ATGGATTTCA GAATCGGACA AGGCTACGAC GTGCACCAGC TCGTTCCCGG ACGCCCGCTC ATCATCGGCG GCGTGACGAT CCCTTACGAG CGGGGGCTGC TCGGCCACTC GGACGCCGAC GTGCTGCTGC ACGCGATCAC CGACGCGCTC TTCGGCGCGG CGGCGCTCGG CGACATCGGC CGCCACTTCT CCGACACCGA TCCGCGCTTC AAGGGCGCCG ACAGCCGCGC GCTGTTGCGC GAATGCGCAT CGCGCGTCGC GCAGGCGGGT TTTGCGATCC GCAACGTCGA CAGCACGATC ATCGCGCAGG CGCCGAAGCT CGCGCCGCAT ATCGACGCGA TGCGCGCGAA CATCGCGGCC GATCTCGACT TGCCGCTCGA TCGCGTGAAC GTGAAGGCGA AGACGAACGA GAAGCTCGGC TATCTCGGGC GCGGTGAGGG GATCGAGGCG CAGGCGGCCG CGCTCGTCGT GCGCGAAGCG GCCGCG

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