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PDBsum entry 2wc6
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protein ligands metals links
Transport protein PDB id
2wc6

 

 

 

 

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Contents
Protein chain
141 a.a. *
Ligands
BOM
Metals
_MG
Waters ×121
* Residue conservation analysis
PDB id:
2wc6
Name: Transport protein
Title: Structure of bmori gobp2 (general odorant binding protein 2) with bombykol and water to arg 110
Structure: General odorant-binding protein 1. Chain: a. Fragment: residues 20-160. Synonym: gobp2, gobp1, general odorant binding protein 2. Engineered: yes
Source: Bombyx mori. Silk moth. Organism_taxid: 7091. Organ: antenna. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.171     R-free:   0.231
Authors: G.Robertson,J.-J.Zhou,X.He,J.A.Pickett,L.M.Field,N.H.Keep
Key ref:
J.J.Zhou et al. (2009). Characterisation of Bombyx mori Odorant-Binding Proteins Reveals that a 'General Odorant-Binding Protein' Discriminates Between Sex Pheromone Components. J Mol Biol, 389, 529-545. PubMed id: 19371749 DOI: 10.1016/j.jmb.2009.04.015
Date:
09-Mar-09     Release date:   11-Aug-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P34170  (OBP2_BOMMO) -  General odorant-binding protein 2 from Bombyx mori
Seq:
Struc: 		160 a.a.
141 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1016/j.jmb.2009.04.015 J Mol Biol 389:529-545 (2009)
PubMed id: 19371749  
 
 
Characterisation of Bombyx mori Odorant-Binding Proteins Reveals that a 'General Odorant-Binding Protein' Discriminates Between Sex Pheromone Components.
J.J.Zhou, G.Robertson, X.He, S.Dufour, A.M.Hooper, J.A.Pickett, N.H.Keep, L.M.Field.
 
  ABSTRACT  
 
In many insect species odorant-binding proteins (OBPs) are thought to be responsible for the transport of pheromones and other semiochemicals across the sensillum lymph to the olfactory receptors (ORs) within the antennal sensilla. In the silkworm Bombyx mori the OBPs are subdivided into three main subfamlies, pheromone-binding proteins (PBPs), general odorant-binding proteins (GOBPs) and antennal binding proteins (ABPs). We used the 'MotifSearch' algorithm to search for genes encoding putative OBPs in B. mori and found 13, many fewer than are found in the genomes of fruitflies and mosquitoes. The 13 genes include seven new ABP-like OBPs as well as the previously identified PBPs (three), GOBPs (two) and ABPx. Quantitative examination of transcript levels showed that BmorPBP1, BmorGOBP1, BmorGOBP2 and BmorABPx are expressed at very high levels in the antennae and so could be involved in olfaction. A new two-phase binding assay, along with other established assays, showed that BmorPBP1, BmorPBP2, BmorGOBP2 and BmorABPx all bind to the B. mori sex pheromone component (10E,12Z)-hexadecadien-1-ol (bombykol). BmorPBP1, BmorPBP2 and BmorABPx also bind the pheromone component (10E,12Z)-hexadecadienal (bombykal) equally well, whereas BmorGOBP2 can discriminate between bombykol and bombykal. X-ray structures show that when bombykol is bound to BmorGOBP2 it adopts a different conformation from that found when it binds to BmorPBP1. Binding to BmorGOBP2 involves hydrogen bonding to Arg110 rather than to the Ser56 as found for BmorPBP1.
 
  Selected figure(s)  
 
Figure 8.
Fig. 8. 3D structures of BmorGOBPs with ligands. (a) A stereo view of the BmorGOBP2 liganded and apo structures. Bombykol (blue), bombykal (coral), (10E,12Z)-tetradecadien-1-ol (yellow), (10E)-hexadecen-12-yn-1-ol (cyan), (8E,10Z)-hexadecadien-1-ol (magenta), apo (black). The bombykol ligand is shown in sphere representation. N and C termini and periodic residues are as indicated in the right-hand image. (b) A stereo view of bombykol plus water structure of BmorGOPB2 with the final 2F[obs] – F[cal] map in pink contoured at 1.0σ clipped to the ligand and water, and the F[obs] – F[cal] map before modelling the ligand contoured at 2.3σ unclipped in green. The side chains of GOBP2 are shown in green. Ser56 and the bombykol of the SSM superposed structure of BmorPBP1 (1dqe) are shown in blue. (c) The F[obs] – F[cal] electron density maps (represented as blue chickenwire) for the BmorGOBP2 ligands before the ligands were added to the structure contoured at 2.3σ. (i) Bombykol coordinated directly to Arg110 and to the main chain carbonyl of Val66. (ii) Bombykol coordinated via a water molecule. (iii) Bombykal, coordinated to a water molecule that is also coordinated to Glu98. (iv) (8E,10Z)-Hexadecadien-1-ol, coordinated both to Glu98 and water. (v) (10E)-Hexadecen-12-yn-1-ol, coordinated to water and Glu98. (vi) (10E,12Z)-Tetradecadien-1-ol, coordinated to Glu98 and water. Hydrogen bonds are indicated as broken black lines as predicted by the algorithm of the CCP4MG molecular graphics program. 		Figure 9.
Fig. 9. Superposition of BmorPBP1 (PDB code 1DQE) and BmorGOBP2 to show structural differences. (a) A stereo pair of BmorPBP1 (red), BmorGOBP2 (blue with regions of greatest difference in light blue). The disulfide bonds are yellow. The bombykol ligand is represented as cylinders and coloured light blue for the BmorGOBP2-bound conformation and pink for the BmorPBP1-bound conformation. The ligand hydrogen bonding residues Ser56 for BmorPBP1 and Arg110 for BmorGOBP2 are shown as green cylinders. (b) (i) Enlarged and simplified view of the major structural difference in the rear entry region (C-termini from residue 126 and residues 25-49). Features are coloured as described above. A potentially important stabilising hydrogen bonding network has been included for BmorPBP1 (Tyr41 and Glu32, shown as pink cylinders). The equivalent Phe41 in BmorGOBP2 (shown as blue cylinders) is buried more deeply and occupies the space of the helix in BmorPBP1. The equivalent region of BmorGOBP2 bulges out to occupy the space filled by the C-terminus of BmorPBP1. (ii) Cut-away view of the ligand-binding pocket showing the key hydrogen bonds formed with the bombykol hydroxyl. PBP1 in red/pink and GOBP2 in blue. Hydrogen bonding side chains are in green. (c) A representation of the possible hydrogen bonding modes of bombykol and bombykal with hydrogen bonds shown as dotted lines. (i) The hydroxyl of bombykol able to form hydrogen bonds to water and to Glu98; and (ii) the aldehyde of bombykal able to form only a single hydrogen bond to water.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 389, 529-545) copyright 2009.  
  Figures were selected by the author.  
 
 
    Author's comment    
 
  The figure shows BmorGOBP2, a general odorant binding protein of the silkmoth Bombyx mori, bind the sex pheromone bombykol more tightly than its aldehyde analogue bombykal because i) The hydroxyl of bombykol able to form two hydrogen bonds to water and to Glu98 and (ii) the aldehyde of bombykal able to form only a single hydrogen bond to water.
Jing-Jiang Zhou, Ph.D. Centre for Sustainable Pest and Disease Management Insect Molecular Biology Group Biological Chemistry Division Rothamsted Research Harpenden AL5 2JQ, UK Email: jing-jiang.zhou@bbsrc.ac.uk http://www.rothamsted.ac.uk/bch/PersonalWebpage/JingJiangPubList.html
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20946532 G.Wang, G.M.Vásquez, C.Schal, L.J.Zwiebel, and F.Gould (2011).
Functional characterization of pheromone receptors in the tobacco budworm Heliothis virescens.
  Insect Mol Biol, 20, 125-133.  
  21541988 S.H.Gu, W.X.Wang, G.R.Wang, X.Y.Zhang, Y.Y.Guo, Z.Zhang, J.J.Zhou, and Y.J.Zhang (2011).
Functional characterization and immunolocalization of odorant binding protein 1 in the lucerne plant bug, Adelphocoris lineolatus (GOEZE).
  Arch Insect Biochem Physiol, 77, 81-99.  
21184151 S.Zhang, L.Z.Chen, S.H.Gu, J.J.Cui, X.W.Gao, Y.J.Zhang, and Y.Y.Guo (2011).
Binding Characterization of Recombinant Odorant-binding Proteins from the Parasitic Wasp, Microplitis mediator (Hymenoptera: Braconidae).
  J Chem Ecol, 37, 189-194.  
21396914 T.Zhang, S.Gu, K.Wu, Y.Zhang, and Y.Guo (2011).
Construction and analysis of cDNA libraries from the antennae of male and female cotton bollworms Helicoverpa armigera (Hübner) and expression analysis of putative odorant-binding protein genes.
  Biochem Biophys Res Commun, 407, 393-399.  
20002214 G.Burns, M.A.Thorne, G.Hillyard, M.S.Clark, P.Convey, and M.R.Worland (2010).
Gene expression associated with changes in cold tolerance levels of the Antarctic springtail, Cryptopygus antarcticus.
  Insect Mol Biol, 19, 113-120.  
20074338 H.Vogel, A.J.Heidel, D.G.Heckel, and A.T.Groot (2010).
Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens.
  BMC Genomics, 11, 29.  
20119869 J.A.Pickett, M.A.Birkett, S.Y.Dewhirst, J.G.Logan, M.O.Omolo, B.Torto, J.Pelletier, Z.Syed, and W.S.Leal (2010).
Chemical ecology of animal and human pathogen vectors in a changing global climate.
  J Chem Ecol, 36, 113-121.  
20482644 J.J.Zhou, F.G.Vieira, X.L.He, C.Smadja, R.Liu, J.Rozas, and L.M.Field (2010).
Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum.
  Insect Mol Biol, 19, 113-122.  
20572127 P.U.Olafson, K.H.Lohmeyer, and S.E.Dowd (2010).
Analysis of expressed sequence tags from a significant livestock pest, the stable fly (Stomoxys calcitrans), identifies transcripts with a putative role in chemosensation and sex determination.
  Arch Insect Biochem Physiol, 74, 179-204.  
20012146 R.Liu, S.Lehane, X.He, M.Lehane, C.Hertz-Fowler, M.Berriman, J.A.Pickett, L.M.Field, and J.J.Zhou (2010).
Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans.
  Cell Mol Life Sci, 67, 919-929.  
20981477 X.He, G.Tzotzos, C.Woodcock, J.A.Pickett, T.Hooper, L.M.Field, and J.J.Zhou (2010).
Binding of the general odorant binding protein of Bombyx mori BmorGOBP2 to the moth sex pheromone components.
  J Chem Ecol, 36, 1293-1305.  
20535533 Z.Liu, D.M.Vidal, Z.Syed, Y.Ishida, and W.S.Leal (2010).
Pheromone binding to general odorant-binding proteins from the navel orangeworm.
  J Chem Ecol, 36, 787-794.  
19774249 A.M.Hooper, S.Dufour, X.He, A.Muck, J.J.Zhou, R.Almeida, L.M.Field, A.Svatos, and J.A.Pickett (2009).
High-throughput ESI-MS analysis of binding between the Bombyx mori pheromone-binding protein BmorPBP1, its pheromone components and some analogues.
  Chem Commun (Camb), (), 5725-5727.  
19960683 C.T.Smartt, and J.S.Erickson (2009).
Expression of a novel member of the odorant-binding protein gene family in Culex nigripalpus (Diptera: Culicidae).
  J Med Entomol, 46, 1376-1381.  
19697043 K.E.Kaissling (2009).
Olfactory perireceptor and receptor events in moths: a kinetic model revised.
  J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 195, 895-922.  
20034407 Y.L.Xu, P.He, L.Zhang, S.Q.Fang, S.L.Dong, Y.J.Zhang, and F.Li (2009).
Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects.
  BMC Genomics, 10, 632.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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