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PDBsum entry 3kmb

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protein ligands metals Protein-protein interface(s) links
Lectin PDB id
3kmb
Jmol
Contents
Protein chains
149 a.a. *
Ligands
SGA-MAG-FUC
FUC
SGA-NAG-FUC
Metals
_CL ×3
_CA ×10
Waters ×458
* Residue conservation analysis
PDB id:
3kmb
Name: Lectin
Title: Complex of 3'-sulfo-lewis-x with a selectin-like mutant of m binding protein a
Structure: Mannose-binding protein-a. Chain: 1, 2, 3. Fragment: clostripain fragment. Synonym: k3. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.95Å     R-factor:   0.204     R-free:   0.254
Authors: K.K.-S.Ng,W.I.Weis
Key ref:
K.K.Ng and W.I.Weis (1997). Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides. Biochemistry, 36, 979-988. PubMed id: 9033386 DOI: 10.1021/bi962564e
Date:
07-Nov-96     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19999  (MBL1_RAT) -  Mannose-binding protein A
Seq:
Struc:
238 a.a.
149 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1021/bi962564e Biochemistry 36:979-988 (1997)
PubMed id: 9033386  
 
 
Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides.
K.K.Ng, W.I.Weis.
 
  ABSTRACT  
 
Rat serum mannose-binding protein in which residues 211-213 have been changed to the Lys-Lys-Lys sequence found in E-selectin binds HL-60 cells and the oligosaccharide 3'-NeuAc-Le(x). To understand how this mutant, designated K3, mimics the carbohydrate-binding properties of E-selectin, structures of K3 alone and in complexes with 3'-NeuAc-Le(x), 3'-sulfo-Le(x) and 4'-sulfo-Le(x) have been determined at 1.95-2.1 A resolution by X-ray crystallography. The region of K3 that interacts with bound oligosaccharides superimposes closely with the corresponding region of unliganded E-selectin. In each of the oligosaccharide-protein complexes, the 2- and 3-OH of Fuc coordinate Ca2+ and form a network of cooperative hydrogen bonds with amino acid side chains that also coordinate the Ca2+. Lys211 of the K3 mutant, which corresponds to Lys111 of E-selectin, interacts with each of the three bound ligands: the N zeta atom donates a hydrogen bond to the 4-OH of Gal in 3'-NeuAc-Le(x), forms a water-mediated hydrogen bond with the 4-OH of Gal in 3'-sulfo-Le(x), and forms a salt bridge with the sulfate group of 4'-sulfo-Le(x). Lys213 packs against an otherwise exposed aromatic residue and forms a water-mediated hydrogen bond with Lys211 which may help to position that residue for interactions with bound oligosaccharides. These structures are consistent with previous mutagenesis and chemical modification studies which demonstrate the importance of the Ca2+ ligands as well as Lys111 and Lys113 for carbohydrate binding in the selectins, and they provide a structural basis for understanding the selective recognition of negatively charged Le(x) derivatives by the selectins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19101969 A.Burkhardt, E.T.Spielberg, S.Simon, H.Görls, A.Buchholz, and W.Plass (2009).
Hydrogen Bonds as Structural Directive towards Unusual Polynuclear Complexes: Synthesis, Structure, and Magnetic Properties of Copper(II) and Nickel(II) Complexes with a 2-Aminoglucose Ligand.
  Chemistry, 15, 1261-1271.  
  18652681 A.S.Gambaryan, A.B.Tuzikov, G.V.Pazynina, J.A.Desheva, N.V.Bovin, M.N.Matrosovich, and A.I.Klimov (2008).
6-sulfo sialyl Lewis X is the common receptor determinant recognized by H5, H6, H7 and H9 influenza viruses of terrestrial poultry.
  Virol J, 5, 85.  
16734974 K.L.White, T.Rades, R.H.Furneaux, P.C.Tyler, and S.Hook (2006).
Mannosylated liposomes as antigen delivery vehicles for targeting to dendritic cells.
  J Pharm Pharmacol, 58, 729-737.  
15780877 A.Gambaryan, S.Yamnikova, D.Lvov, A.Tuzikov, A.Chinarev, G.Pazynina, R.Webster, M.Matrosovich, and N.Bovin (2005).
Receptor specificity of influenza viruses from birds and mammals: new data on involvement of the inner fragments of the carbohydrate chain.
  Virology, 334, 276-283.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15184372 E.Van Liempt, A.Imberty, C.M.Bank, S.J.Van Vliet, Y.Van Kooyk, T.B.Geijtenbeek, and I.Van Die (2004).
Molecular basis of the differences in binding properties of the highly related C-type lectins DC-SIGN and L-SIGN to Lewis X trisaccharide and Schistosoma mansoni egg antigens.
  J Biol Chem, 279, 33161-33167.  
12369089 N.Kaila, and B.E.Thomas (2002).
Design and synthesis of sialyl Lewis(x) mimics as E- and P-selectin inhibitors.
  Med Res Rev, 22, 566-601.  
11960993 S.Bouyain, N.J.Silk, G.Fabini, and K.Drickamer (2002).
An endogenous Drosophila receptor for glycans bearing alpha 1,3-linked core fucose residues.
  J Biol Chem, 277, 22566-22572.  
11159435 D.F.Tees, R.E.Waugh, and D.A.Hammer (2001).
A microcantilever device to assess the effect of force on the lifetime of selectin-carbohydrate bonds.
  Biophys J, 80, 668-682.  
11251878 L.Nitschke, H.Floyd, and P.R.Crocker (2001).
New functions for the sialic acid-binding adhesion molecule CD22, a member of the growing family of Siglecs.
  Scand J Immunol, 53, 227-234.  
11454337 T.Tanase, T.Takei, M.Hidai, and S.Yano (2001).
Substrate-dependent chemoselective aldose-aldose and aldose-ketose isomerizations of carbohydrates promoted by a combination of calcium ion and monoamines.
  Carbohydr Res, 333, 303-312.  
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
10748229 Y.Liu, A.J.Chirino, Z.Misulovin, C.Leteux, T.Feizi, M.C.Nussenzweig, and P.J.Bjorkman (2000).
Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.
  J Exp Med, 191, 1105-1116.
PDB codes: 1dqg 1dqo
10410803 C.A.Bush, M.Martin-Pastor, and A.Imberty (1999).
Structure and conformation of complex carbohydrates of glycoproteins, glycolipids, and bacterial polysaccharides.
  Annu Rev Biophys Biomol Struct, 28, 269-293.  
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
9660955 A.P.May, R.C.Robinson, M.Vinson, P.R.Crocker, and E.Y.Jones (1998).
Crystal structure of the N-terminal domain of sialoadhesin in complex with 3' sialyllactose at 1.85 A resolution.
  Mol Cell, 1, 719-728.
PDB codes: 1qfo 1qfp
9497351 D.Torgersen, N.P.Mullin, and K.Drickamer (1998).
Mechanism of ligand binding to E- and P-selectin analyzed using selectin/mannose-binding protein chimeras.
  J Biol Chem, 273, 6254-6261.  
9922165 K.K.Ng, S.Park-Snyder, and W.I.Weis (1998).
Ca2+-dependent structural changes in C-type mannose-binding proteins.
  Biochemistry, 37, 17965-17976.
PDB codes: 1buu 1bv4
9922166 K.K.Ng, and W.I.Weis (1998).
Coupling of prolyl peptide bond isomerization and Ca2+ binding in a C-type mannose-binding protein.
  Biochemistry, 37, 17977-17989.  
9695813 M.J.Humphries, and P.Newham (1998).
The structure of cell-adhesion molecules.
  Trends Cell Biol, 8, 78-83.  
9700499 W.I.Weis, M.E.Taylor, and K.Drickamer (1998).
The C-type lectin superfamily in the immune system.
  Immunol Rev, 163, 19-34.  
9345618 A.Imberty (1997).
Oligosaccharide structures: theory versus experiment.
  Curr Opin Struct Biol, 7, 617-623.  
9345617 J.Rini, and K.Drickamer (1997).
Carbohydrates and glycoconjugates.
  Curr Opin Struct Biol, 7, 615-616.  
9345619 W.I.Weis (1997).
Cell-surface carbohydrate recognition by animal and viral lectins.
  Curr Opin Struct Biol, 7, 624-630.  
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 codes are shown on the right.