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PDBsum entry 1lob
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protein ligands metals Protein-protein interface(s) links
Lectin PDB id
1lob

 

 

 

 

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Contents
Protein chains
180 a.a. *
47 a.a. *
47 a.a. *
Ligands
MMA ×4
Metals
_MN ×4
_CA ×4
Waters ×298
* Residue conservation analysis
PDB id:
1lob
Name: Lectin
Title: Three-dimensional structures of complexes of lathyrus ochrus isolectin i with glucose and mannose: fine specificity of the monosaccharide- binding site
Structure: Legume isolectin i (alpha chain). Chain: a, c, e, g. Engineered: yes. Legume isolectin i (beta chain). Chain: b, d, f, h. Engineered: yes
Source: Lathyrus ochrus. Yellow-flowered pea. Organism_taxid: 3858. Organ: seed. Organ: seed
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.182    
Authors: Y.Bourne,C.Cambillau
Key ref: Y.Bourne et al. (1990). Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site. Proteins, 8, 365-376. PubMed id: 2091026
Date:
27-Jan-93     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04122  (LECB_LATOC) -  Lectin beta-1 and beta-2 chains from Lathyrus ochrus
Seq:
Struc: 		181 a.a.
180 a.a.*
Protein chains
P12306  (LEC1_LATOC) -  Mannose/glucose-specific lectin alpha 1 chain from Lathyrus ochrus
Seq:
Struc: 		53 a.a.
47 a.a.*
Protein chains
P12306  (LEC1_LATOC) -  Mannose/glucose-specific lectin alpha 1 chain from Lathyrus ochrus
Seq:
Struc: 		53 a.a.
47 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Proteins 8:365-376 (1990)
PubMed id: 2091026  
 
 
Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site.
Y.Bourne, A.Roussel, M.Frey, P.Rougé, J.C.Fontecilla-Camps, C.Cambillau.
 
  ABSTRACT  
 
The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo greater than 1 sigma(Fo)]. The isostructural methyl-alpha-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-alpha-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Waals contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21277932 B.A.Rocha, P.Delatorre, T.M.Oliveira, R.G.Benevides, A.F.Pires, A.A.Sousa, L.A.Souza, A.M.Assreuy, H.Debray, W.F.de Azevedo, A.H.Sampaio, and B.S.Cavada (2011).
Structural basis for both pro- and anti-inflammatory response induced by mannose-specific legume lectin from Cymbosema roseum.
  Biochimie, 93, 806-816.
PDB code: 3a0k
18720336 E.J.Cocinero, E.C.Stanca-Kaposta, E.M.Scanlan, D.P.Gamblin, B.G.Davis, and J.P.Simons (2008).
Conformational choice and selectivity in singly and multiply hydrated monosaccharides in the gas phase.
  Chemistry, 14, 8947-8955.  
18045876 G.Sciara, S.Blangy, M.Siponen, S.Mc Grath, D.van Sinderen, M.Tegoni, C.Cambillau, and V.Campanacci (2008).
A topological model of the baseplate of lactococcal phage tuc2009.
  J Biol Chem, 283, 2716-2723.  
18393823 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2008).
Structure and function of beta -1,4-galactosyltransferase.
  Curr Drug Targets, 9, 292-309.  
16547026 D.M.Tremblay, M.Tegoni, S.Spinelli, V.Campanacci, S.Blangy, C.Huyghe, A.Desmyter, S.Labrie, S.Moineau, and C.Cambillau (2006).
Receptor-binding protein of Lactococcus lactis phages: identification and characterization of the saccharide receptor-binding site.
  J Bacteriol, 188, 2400-2410.
PDB code: 1zru
16584127 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2006).
Mutant glycosyltransferases assist in the development of a targeted drug delivery system and contrast agents for MRI.
  AAPS J, 8, E190-E195.  
16940545 S.Ricagno, V.Campanacci, S.Blangy, S.Spinelli, D.Tremblay, S.Moineau, M.Tegoni, and C.Cambillau (2006).
Crystal structure of the receptor-binding protein head domain from Lactococcus lactis phage bIL170.
  J Virol, 80, 9331-9335.
PDB code: 2fsd
16327804 S.Spinelli, A.Desmyter, C.T.Verrips, H.J.de Haard, S.Moineau, and C.Cambillau (2006).
Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses.
  Nat Struct Mol Biol, 13, 85-89.
PDB codes: 2bsd 2bse
16439369 T.Satoh, K.Sato, A.Kanoh, K.Yamashita, Y.Yamada, N.Igarashi, R.Kato, A.Nakano, and S.Wakatsuki (2006).
Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
  J Biol Chem, 281, 10410-10419.
PDB codes: 2a6v 2a6w 2a6x 2a6y 2a6z 2a70 2a71
12595543 R.Loris, A.Imberty, S.Beeckmans, E.Van Driessche, J.S.Read, J.Bouckaert, H.De Greve, L.Buts, and L.Wyns (2003).
Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose.
  J Biol Chem, 278, 16297-16303.
PDB codes: 1n3o 1n3p 1n3q
11786557 L.J.Olson, J.Zhang, N.M.Dahms, and J.J.Kim (2002).
Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptor.
  J Biol Chem, 277, 10156-10161.
PDB code: 1keo
11850423 L.M.Velloso, K.Svensson, G.Schneider, R.F.Pettersson, and Y.Lindqvist (2002).
Crystal structure of the carbohydrate recognition domain of p58/ERGIC-53, a protein involved in glycoprotein export from the endoplasmic reticulum.
  J Biol Chem, 277, 15979-15984.
PDB code: 1gv9
11484224 A.Rabijns, C.Verboven, P.Rougé, A.Barre, E.J.Van Damme, W.J.Peumans, and C.J.De Ranter (2001).
Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine.
  Proteins, 44, 470-478.
PDB codes: 1fny 1fnz
11288176 R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, and M.Vijayan (2001).
Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.
  Proteins, 43, 260-270.
PDB codes: 1cq9 1cqb 1cr7
  10338018 E.García-Hernández, and A.Hernández-Arana (1999).
Structural bases of lectin-carbohydrate affinities: comparison with protein-folding energetics.
  Protein Sci, 8, 1075-1086.  
10089310 N.Manoj, V.R.Srinivas, and K.Suguna (1999).
Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.
  Acta Crystallogr D Biol Crystallogr, 55, 794-800.
PDB code: 1wbf
10647178 Y.Bourne, V.Zamboni, A.Barre, W.J.Peumans, E.J.Van Damme, and P.Rougé (1999).
Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins.
  Structure, 7, 1473-1482.
PDB codes: 1c3k 1c3m 1c3n
9582323 L.Mourey, J.D.Pédelacq, C.Birck, C.Fabre, P.Rougé, and J.P.Samama (1998).
Crystal structure of the arcelin-1 dimer from Phaseolus vulgaris at 1.9-A resolution.
  J Biol Chem, 273, 12914-12922.
PDB code: 1avb
9857034 W.Cheng, E.Bullitt, L.Bhattacharyya, C.F.Brewer, and L.Makowski (1998).
Electron microscopy and x-ray diffraction studies of Lotus tetragonolobus A isolectin cross-linked with a divalent Lewisx oligosaccharide, an oncofetal antigen.
  J Biol Chem, 273, 35016-35022.  
9115445 K.Drickamer (1997).
Making a fitting choice: common aspects of sugar-binding sites in plant and animal lectins.
  Structure, 5, 465-468.  
  8868475 C.Itin, A.C.Roche, M.Monsigny, and H.P.Hauri (1996).
ERGIC-53 is a functional mannose-selective and calcium-dependent human homologue of leguminous lectins.
  Mol Biol Cell, 7, 483-493.  
8557713 J.H.Naismith, and R.A.Field (1996).
Structural basis of trimannoside recognition by concanavalin A.
  J Biol Chem, 271, 972-976.
PDB code: 1cvn
8774711 R.Adar, and N.Sharon (1996).
Mutational studies of the amino acid residues in the combining site of Erythrina corallodendron lectin.
  Eur J Biochem, 239, 668-674.  
8955116 T.W.Hamelryck, F.Poortmans, A.Goossens, G.Angenon, M.Van Montagu, L.Wyns, and R.Loris (1996).
Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris.
  J Biol Chem, 271, 32796-32802.
PDB code: 1ioa
7620329 Y.Konami, K.Yamamoto, T.Osawa, and T.Irimura (1995).
A putative carbohydrate-binding domain of the lactose-binding Cytisus sessilifolius anti-H(O) lectin has a similar amino acid sequence to that of the L-fucose-binding Ulex europaeus anti-H(O) lectin.
  Glycoconj J, 12, 128-134.  
7696844 A.Imberty, F.Casset, C.V.Gegg, M.E.Etzler, and S.Pérez (1994).
Molecular modelling of the Dolichos biflorus seed lectin and its specific interactions with carbohydrates: alpha-D-N-acetyl-galactosamine, Forssman disaccharide and blood group A trisaccharide.
  Glycoconj J, 11, 400-413.  
7731952 R.Loris, D.Van Overberge, M.H.Dao-Thi, F.Poortmans, N.Maene, and L.Wyns (1994).
Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.
  Proteins, 20, 330-346.
PDB codes: 1len 2lal
7696853 R.Loris, F.Casset, J.Bouckaert, J.Pletinckx, M.H.Dao-Thi, F.Poortmans, A.Imberty, S.Perez, and L.Wyns (1994).
The monosaccharide binding site of lentil lectin: an X-ray and molecular modelling study.
  Glycoconj J, 11, 507-517.
PDB code: 1lem
8069634 Y.Bourne, J.Mazurier, D.Legrand, P.Rougé, J.Montreuil, G.Spik, and C.Cambillau (1994).
Structures of a legume lectin complexed with the human lactotransferrin N2 fragment, and with an isolated biantennary glycopeptide: role of the fucose moiety.
  Structure, 2, 209-219.
PDB codes: 1lgb 1lgc
8346557 N.Sharon (1993).
Lectin-carbohydrate complexes of plants and animals: an atomic view.
  Trends Biochem Sci, 18, 221-226.  
1422132 A.Ayouba, H.Debray, and P.Rougé (1992).
Fine sugar specificity of the Butea frondosa seed lectin.
  Glycoconj J, 9, 141-147.  
1376919 J.K.Scott, D.Loganathan, R.B.Easley, X.Gong, and I.J.Goldstein (1992).
A family of concanavalin A-binding peptides from a hexapeptide epitope library.
  Proc Natl Acad Sci U S A, 89, 5398-5402.  
1893996 A.Ayouba, C.Chatelain, and P.Rougé (1991).
Legume lectins interact with muramic acid and N-acetylmuramic acid.
  FEBS Lett, 289, 102-104.  
1367679 J.A.Tainer, V.A.Roberts, and E.D.Getzoff (1991).
Metal-binding sites in proteins.
  Curr Opin Biotechnol, 2, 582-591.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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