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

 

 

 

 

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Contents
Protein chains
111 a.a. *
Ligands
MMA ×3
Metals
_CL
_CA ×4
Waters ×308
* Residue conservation analysis
PDB id:
1rdm
Name: Lectin
Title: Mannose-binding protein, subtilisin digest fragment complex with alpha-methyl-d-mannopyranoside (1.3 m)
Structure: Mannose-binding protein-c. Chain: 1, 2. Fragment: subtilisin fragment (residues 114 - 226). Synonym: sub-mbp-c. Engineered: yes
Source: Rattus rattus. Black rat. Organism_taxid: 10117. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the bacterially expressed material is digested with subtilisin to produce the protein used in the crystal structure analysis
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.191     R-free:   0.240
Authors: K.K.-S.Ng,K.Drickamer,W.I.Weis
Key ref: K.K.Ng et al. (1996). Structural analysis of monosaccharide recognition by rat liver mannose-binding protein. J Biol Chem, 271, 663-674. PubMed id: 8557671
Date:
05-Sep-95     Release date:   08-Mar-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08661  (MBL2_RAT) -  Mannose-binding protein C from Rattus norvegicus
Seq:
Struc: 		244 a.a.
111 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
J Biol Chem 271:663-674 (1996)
PubMed id: 8557671  
 
 
Structural analysis of monosaccharide recognition by rat liver mannose-binding protein.
K.K.Ng, K.Drickamer, W.I.Weis.
 
  ABSTRACT  
 
The structural basis of carbohydrate recognition by rat liver mannose-binding protein (MBP-C) has been explored by determining the three-dimensional structure of the C-type carbohydrate-recognition domain (CRD) of MBP-C using x-ray crystallography. The structure was solved by molecular replacement using rat serum mannose-binding protein (MBP-A) as a search model and was refined to maximum Bragg spacings of 1.7 A. Despite their almost identical folds, the dimeric structures formed by the two MBP CRDs differ dramatically. Complexes of MBP-C with methyl glycosides of mannose, N-acetylglucosamine, and fucose were prepared by soaking MBP-C crystals in solutions containing these sugars. Surprisingly, the pyranose ring of mannose is rotated 180 degrees relative to the orientation observed previously in MBP-A, but the local interactions between sugar and protein are preserved. For each of the bound sugars, vicinal, equatorial hydroxyl groups equivalent to the 3- and 4-OH groups of mannose directly coordinate Ca2+ and form hydrogen bonds with residues also serving as Ca2+ ligands. Few interactions are observed between other parts of the sugar and the protein. A complex formed between free galactose and MBP-C reveals a similar mode of binding, with the anomeric hydroxyl group serving as one of the Ca2+ ligands. A second binding site for mannose has also been observed in one of two copies in the asymmetric unit at a sugar concentration of 1.3 M. These structures explain how MBPs recognize a wide range of monosaccharides and suggest how fine specificity differences between MBP-A and MBP-C may be achieved.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21112966 R.T.Lee, T.L.Hsu, S.K.Huang, S.L.Hsieh, C.H.Wong, and Y.C.Lee (2011).
Survey of immune-related, mannose/fucose-binding C-type lectin receptors reveals widely divergent sugar-binding specificities.
  Glycobiology, 21, 512-520.  
19610105 M.Uittenbogaard, K.K.Baxter, and A.Chiaramello (2010).
NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network.
  J Neurosci Res, 88, 33-54.  
19799916 A.K.Shrive, C.Martin, I.Burns, J.M.Paterson, J.D.Martin, J.P.Townsend, P.Waters, H.W.Clark, U.Kishore, K.B.Reid, and T.J.Greenhough (2009).
Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.
  J Mol Biol, 394, 776-788.
PDB codes: 3ikn 3ikp 3ikq 3ikr
17420244 H.Feinberg, M.E.Taylor, and W.I.Weis (2007).
Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.
  J Biol Chem, 282, 17250-17258.
PDB codes: 2ox8 2ox9
17150970 H.Feinberg, R.Castelli, K.Drickamer, P.H.Seeberger, and W.I.Weis (2007).
Multiple modes of binding enhance the affinity of DC-SIGN for high mannose N-linked glycans found on viral glycoproteins.
  J Biol Chem, 282, 4202-4209.
PDB codes: 2it5 2it6
17363917 M.Møller-Kristensen, M.R.Hamblin, S.Thiel, J.C.Jensenius, and K.Takahashi (2007).
Burn injury reveals altered phenotype in mannan-binding lectin-deficient mice.
  J Invest Dermatol, 127, 1524-1531.  
16897175 R.T.Lee, and Y.C.Lee (2006).
Carbohydrate ligands of human C-reactive protein: binding of neoglycoproteins containing galactose-6-phosphate and galactose-terminated disaccharide.
  Glycoconj J, 23, 317-327.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
16237644 K.Takahashi, and R.A.Ezekowitz (2005).
The role of the mannose-binding lectin in innate immunity.
  Clin Infect Dis, 41, S440-S444.  
15030473 J.K.van de Wetering, L.M.van Golde, and J.J.Batenburg (2004).
Collectins: players of the innate immune system.
  Eur J Biochem, 271, 1229-1249.  
15148336 L.Shi, K.Takahashi, J.Dundee, S.Shahroor-Karni, S.Thiel, J.C.Jensenius, F.Gad, M.R.Hamblin, K.N.Sastry, and R.A.Ezekowitz (2004).
Mannose-binding lectin-deficient mice are susceptible to infection with Staphylococcus aureus.
  J Exp Med, 199, 1379-1390.  
15195147 Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, and K.Drickamer (2004).
Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR.
  Nat Struct Mol Biol, 11, 591-598.
PDB codes: 1sl4 1sl5 1sl6
11964255 E.W.Sayers, and J.H.Prestegard (2002).
Conformation of a trimannoside bound to mannose-binding protein by nuclear magnetic resonance and molecular dynamics simulations.
  Biophys J, 82, 2683-2699.  
12417723 S.J.Lee, G.Gonzalez-Aseguinolaza, and M.C.Nussenzweig (2002).
Disseminated candidiasis and hepatic malarial infection in mannose-binding-lectin-A-deficient mice.
  Mol Cell Biol, 22, 8199-8203.  
11785767 H.Kogelberg, and T.Feizi (2001).
New structural insights into lectin-type proteins of the immune system.
  Curr Opin Struct Biol, 11, 635-643.  
11425305 M.J.Allen, A.Laederach, P.J.Reilly, and R.J.Mason (2001).
Polysaccharide recognition by surfactant protein D: novel interactions of a C-type lectin with nonterminal glucosyl residues.
  Biochemistry, 40, 7789-7798.  
11667972 E.C.Crouch (2000).
Surfactant protein-D and pulmonary host defense.
  Respir Res, 1, 93.  
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
10931211 K.Mann, I.M.Weiss, S.André, H.J.Gabius, and M.Fritz (2000).
The amino-acid sequence of the abalone (Haliotis laevigata) nacre protein perlucin. Detection of a functional C-type lectin domain with galactose/mannose specificity.
  Eur J Biochem, 267, 5257-5264.  
  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.  
10023772 J.C.Boyington, A.N.Riaz, A.Patamawenu, J.E.Coligan, A.G.Brooks, and P.D.Sun (1999).
Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors.
  Immunity, 10, 75-82.
PDB code: 1b6e
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
10368295 K.Håkansson, N.K.Lim, H.J.Hoppe, and K.B.Reid (1999).
Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D.
  Structure, 7, 255-264.
PDB code: 1b08
10607664 M.Vijayan, and N.Chandra (1999).
Lectins.
  Curr Opin Struct Biol, 9, 707-714.  
9437428 D.Forst, W.Welte, T.Wacker, and K.Diederichs (1998).
Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
  Nat Struct Biol, 5, 37-46.
PDB codes: 1a0s 1a0t
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.  
9057819 H.J.Gabius (1997).
Animal lectins.
  Eur J Biochem, 243, 543-576.  
9115445 K.Drickamer (1997).
Making a fitting choice: common aspects of sugar-binding sites in plant and animal lectins.
  Structure, 5, 465-468.  
9345619 W.I.Weis (1997).
Cell-surface carbohydrate recognition by animal and viral lectins.
  Curr Opin Struct Biol, 7, 624-630.  
8939757 C.S.Wright, and G.Hester (1996).
The 2.0 A structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes.
  Structure, 4, 1339-1352.
PDB code: 1jpc
8913692 P.R.Crocker, and T.Feizi (1996).
Carbohydrate recognition systems: functional triads in cell-cell interactions.
  Curr Opin Struct Biol, 6, 679-691.  
8710873 S.Karlin, and Z.Y.Zhu (1996).
Characterizations of diverse residue clusters in protein three-dimensional structures.
  Proc Natl Acad Sci U S A, 93, 8344-8349.  
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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