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PDBsum entry 2rib

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protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
2rib
Jmol
Contents
Protein chain
150 a.a. *
Ligands
GMH ×3
Metals
_CA ×9
Waters ×458
* Residue conservation analysis
PDB id:
2rib
Name: Sugar binding protein
Title: Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein d in complex with l-glycero-d-manno-heptose
Structure: Pulmonary surfactant-associated protein d. Chain: a, b, c. Fragment: neck and carbohydrate recognition domain. Synonym: sp-d. Psp-d. Lung surfactant protein d. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sftpd, pspd, sftp4. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.186     R-free:   0.204
Authors: H.Wang,J.Head,P.Kosma,S.Sheikh,B.Mcdonald,K.Smith, T.Cafarella,B.Seaton,E.Crouch
Key ref: H.Wang et al. (2008). Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d. Biochemistry, 47, 710-720. PubMed id: 18092821 DOI: 10.1021/bi7020553
Date:
10-Oct-07     Release date:   15-Jan-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P35247  (SFTPD_HUMAN) -  Pulmonary surfactant-associated protein D
Seq:
Struc:
375 a.a.
150 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1021/bi7020553 Biochemistry 47:710-720 (2008)
PubMed id: 18092821  
 
 
Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.
H.Wang, J.Head, P.Kosma, H.Brade, S.Müller-Loennies, S.Sheikh, B.McDonald, K.Smith, T.Cafarella, B.Seaton, E.Crouch.
 
  ABSTRACT  
 
Lipopolysaccharides (LPS) of Gram-negative bacteria are important mediators of bacterial virulence that can elicit potent endotoxic effects. Surfactant protein D (SP-D) shows specific interactions with LPS, both in vitro and in vivo. These interactions involve binding of the carbohydrate recognition domain (CRD) to LPS oligosaccharides (OS); however, little is known about the mechanisms of LPS recognition. Recombinant neck+CRDs (NCRDs) provide an opportunity to directly correlate binding interactions with a crystallographic analysis of the binding mechanism. In these studies, we examined the interactions of wild-type and mutant trimeric NCRDs with rough LPS (R-LPS). Although rat NCRDs bound more efficiently than human NCRDs to Escherichia coli J-5 LPS, both proteins exhibited efficient binding to solid-phase Rd2-LPS and to Rd2-LPS aggregates presented in the solution phase. Involvement of residues flanking calcium at the sugar binding site was demonstrated by reciprocal exchange of lysine and arginine at position 343 of rat and human CRDs. The lectin activity of hNCRDs was inhibited by specific heptoses, including l-glycero-alpha-d-manno-heptose (l,d-heptose), but not by 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo). Crystallographic analysis of the hNCRD demonstrated a novel binding orientation for l,d-heptose, involving the hydroxyl groups of the side chain. Similar binding was observed for a synthetic alpha1-->3-linked heptose disaccharide corresponding to heptoses I and II of the inner core region in many LPS. 7-O-Carbamoyl-l,d-heptose and d-glycero-alpha-d-manno-heptose were bound via ring hydroxyl groups. Interactions with the side chain of inner core heptoses provide a potential mechanism for the recognition of diverse types of LPS by SP-D.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20004639 R.Mendelsohn, G.Mao, and C.R.Flach (2010).
Infrared reflection-absorption spectroscopy: principles and applications to lipid-protein interaction in Langmuir films.
  Biochim Biophys Acta, 1798, 788-800.  
20054141 Z.C.Chroneos, Z.Sever-Chroneos, and V.L.Shepherd (2010).
Pulmonary surfactant: an immunological perspective.
  Cell Physiol Biochem, 25, 13-26.  
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
19249874 E.Crouch, K.Hartshorn, T.Horlacher, B.McDonald, K.Smith, T.Cafarella, B.Seaton, P.H.Seeberger, and J.Head (2009).
Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343.
  Biochemistry, 48, 3335-3345.
PDB codes: 3g81 3g83 3g84
19244241 J.Mares, S.Kumaran, M.Gobbo, and O.Zerbe (2009).
Interactions of lipopolysaccharide and polymyxin studied by NMR spectroscopy.
  J Biol Chem, 284, 11498-11506.  
19126597 S.Matalon, K.Shrestha, M.Kirk, S.Waldheuser, B.McDonald, K.Smith, Z.Gao, A.Belaaouaj, and E.C.Crouch (2009).
Modification of surfactant protein D by reactive oxygen-nitrogen intermediates is accompanied by loss of aggregating activity, in vitro and in vivo.
  FASEB J, 23, 1415-1430.  
19684355 T.K.Carlson, J.B.Torrelles, K.Smith, T.Horlacher, R.Castelli, P.H.Seeberger, E.C.Crouch, and L.S.Schlesinger (2009).
Critical role of amino acid position 343 of surfactant protein-D in the selective binding of glycolipids from Mycobacterium tuberculosis.
  Glycobiology, 19, 1473-1484.  
18687680 J.P.Gourdine, G.Cioci, L.Miguet, C.Unverzagt, D.V.Silva, A.Varrot, C.Gautier, E.J.Smith-Ravin, and A.Imberty (2008).
High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry.
  J Biol Chem, 283, 30112-30120.
PDB codes: 2vuv 2vuz
18713318 M.Ramjeet, A.D.Cox, M.A.Hancock, M.Mourez, J.Labrie, M.Gottschalk, and M.Jacques (2008).
Mutation in the LPS outer core biosynthesis gene, galU, affects LPS interaction with the RTX toxins ApxI and ApxII and cytolytic activity of Actinobacillus pleuropneumoniae serotype 1.
  Mol Microbiol, 70, 221-235.  
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.