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

 

 

 

 

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Contents
Protein chains
154 a.a. *
Ligands
A2G
NGA ×2
Metals
_CL ×3
_NA
_CA ×9
Waters ×326
* Residue conservation analysis
PDB id:
1bch
Name: Lectin
Title: Mannose-binding protein-a mutant (qpdwgh) complexed with n-acetyl-d- galactosamine
Structure: Mannose-binding protein-a. Chain: 1, 2, 3. Fragment: clostripain fragment residues 73 - 226. Synonym: cl-qpdwgh. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the bacterially expressed material was digested with clostripain to produce the protein used in the crystal structure analysis
Biol. unit: Trimer (from PQS)
Resolution:
2.00Å     R-factor:   0.219     R-free:   0.252
Authors: A.R.Kolatkar,W.I.Weis
Key ref:
A.R.Kolatkar et al. (1998). Mechanism of N-acetylgalactosamine binding to a C-type animal lectin carbohydrate-recognition domain. J Biol Chem, 273, 19502-19508. PubMed id: 9677372 DOI: 10.1074/jbc.273.31.19502
Date:
30-Apr-98     Release date:   17-Jun-98    
PROCHECK
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 Headers
 References

Protein chains
P19999  (MBL1_RAT) -  Mannose-binding protein A from Rattus norvegicus
Seq:
Struc: 		238 a.a.
154 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 

 
DOI no: 10.1074/jbc.273.31.19502 J Biol Chem 273:19502-19508 (1998)
PubMed id: 9677372  
 
 
Mechanism of N-acetylgalactosamine binding to a C-type animal lectin carbohydrate-recognition domain.
A.R.Kolatkar, A.K.Leung, R.Isecke, R.Brossmer, K.Drickamer, W.I.Weis.
 
  ABSTRACT  
 
The mammalian hepatic asialoglycoprotein receptor, a member of the C-type animal lectin family, displays preferential binding to N-acetylgalactosamine compared with galactose. The structural basis for selective binding to N-acetylgalactosamine has been investigated. Regions of the carbohydrate-recognition domain of the receptor believed to be important in preferential binding to N-acetylgalactosamine have been inserted into the homologous carbohydrate-recognition domain of a mannose-binding protein mutant that was previously altered to bind galactose. Introduction of a single histidine residue corresponding to residue 256 of the hepatic asialoglycoprotein receptor was found to cause a 14-fold increase in the relative affinity for N-acetylgalactosamine compared with galactose. The relative ability of various acyl derivatives of galactosamine to compete for binding to this modified carbohydrate-recognition domain suggest that it is a good model for the natural N-acetylgalactosamine binding site of the asialoglycoprotein receptor. Crystallographic analysis of this mutant carbohydrate-recognition domain in complex with N-acetylgalactosamine reveals a direct interaction between the inserted histidine residue and the methyl group of the N-acetyl substituent of the sugar. Evidence for the role of the side chain at position 208 of the receptor in positioning this key histidine residue was obtained from structural analysis and mutagenesis experiments. The corresponding serine residue in the modified carbohydrate-recognition domain of mannose-binding protein forms a hydrogen bond to the imidazole side chain. When this serine residue is changed to valine, loss in selectivity for N-acetylgalactosamine is observed. The structure of this mutant reveals that the beta-branched valine side chain interacts directly with the histidine side chain, resulting in an altered imidazole ring orientation.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Ribbon representation of crystal structure of the QPDWGH mutant of MBP complexed with GalNAc. Stereo ribbon drawing shows the vicinity of the GalNAc binding site with the sugar and selected residues drawn as balls-and-sticks. The glycine-rich loop stacked against Trp189 is highlighted in gray and Ca^2+ 1 and 2 are shown as gray spheres. The hydrogen bond between Ser154 and His202 is drawn as a dashed line. 		Figure 5.
Fig. 5. van der Waals dot surface representation of the GalNAc binding site of the QPDWGH mutant of MBP. Stereo pair shows the GalNAc binding site in an orientation very similar to that in Fig. 4. The His202/GalNAc contact is apparent at the bottom. The stacking of the glycine-rich loop, Trp189 ring, and the apolar face of GalNAc is seen at the top. This figure was prepared with the Xfit component of the XtalView program suite (24).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 19502-19508) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19528664 M.E.Taylor, and K.Drickamer (2009).
Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands.
  Glycobiology, 19, 1155-1162.  
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
17984090 A.S.Powlesland, T.Fisch, M.E.Taylor, D.F.Smith, B.Tissot, A.Dell, S.Pöhlmann, and K.Drickamer (2008).
A novel mechanism for LSECtin binding to Ebola virus surface glycoprotein through truncated glycans.
  J Biol Chem, 283, 593-602.  
18790731 M.Sakakura, S.Oo-Puthinan, C.Moriyama, T.Kimura, J.Moriya, T.Irimura, and I.Shimada (2008).
Carbohydrate binding mechanism of the macrophage galactose-type C-type lectin 1 revealed by saturation transfer experiments.
  J Biol Chem, 283, 33665-33673.  
16507387 C.M.Millar, and S.A.Brown (2006).
Oligosaccharide structures of von Willebrand factor and their potential role in von Willebrand disease.
  Blood Rev, 20, 83-92.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
12471063 S.Radaev, and P.D.Sun (2003).
Structure and function of natural killer cell surface receptors.
  Annu Rev Biophys Biomol Struct, 32, 93.  
12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
9989502 K.L.Mohlke, A.A.Purkayastha, R.J.Westrick, P.L.Smith, B.Petryniak, J.B.Lowe, and D.Ginsburg (1999).
Mvwf, a dominant modifier of murine von Willebrand factor, results from altered lineage-specific expression of a glycosyltransferase.
  Cell, 96, 111-120.  
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.

 

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