spacer
spacer

PDBsum entry 2ork

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
2ork
Jmol
Contents
Protein chain
151 a.a. *
Ligands
IPD ×2
Metals
_CA ×9
Waters ×517
* Residue conservation analysis
PDB id:
2ork
Name: Sugar binding protein
Title: Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein d in complex with inositol-1-phosphate
Structure: Pulmonary surfactant-associated protein d. Chain: a, b, c. Fragment: head and neck 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:
1.89Å     R-factor:   0.190     R-free:   0.226
Authors: J.F.Head
Key ref: E.Crouch et al. (2007). Critical role of Arg/Lys343 in the species-dependent recognition of phosphatidylinositol by pulmonary surfactant protein D. Biochemistry, 46, 5160-5169. PubMed id: 17417879 DOI: 10.1021/bi700037x
Date:
02-Feb-07     Release date:   08-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P35247  (SFTPD_HUMAN) -  Pulmonary surfactant-associated protein D
Seq:
Struc:
375 a.a.
151 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/bi700037x Biochemistry 46:5160-5169 (2007)
PubMed id: 17417879  
 
 
Critical role of Arg/Lys343 in the species-dependent recognition of phosphatidylinositol by pulmonary surfactant protein D.
E.Crouch, B.McDonald, K.Smith, M.Roberts, T.Mealy, B.Seaton, J.Head.
 
  ABSTRACT  
 
Surfactant protein D (SP-D) plays important roles in lung host defense. However, it can also recognize specific host molecules and contributes to surfactant homeostasis. The major known surfactant-associated ligand is phosphatidylinositol (PI). Trimeric neck-carbohydrate recognition domains (NCRDs) of rat and human SP-D exhibited dose-dependent, calcium-dependent, and inositol-sensitive binding to solid-phase PI and to multilamellar PI liposomes. However, the rat protein exhibited a >5-fold higher affinity for solid-phase PI than the human NCRD. In addition, human dodecamers, but not full-length human trimers, efficiently coprecipitated with multilamellar PI liposomes in the presence of calcium. A human NCRD mutant resembling the rat and mouse proteins at position 343 (hR343K) showed much stronger binding to PI. A reciprocal rat mutant with arginine at the position of lysine 343 (rK343R) showed weak binding to PI, even weaker than that of the wild-type human protein. Crystal complexes of the human trimeric NCRD with myoinositol and inositol 1-phosphate showed binding of the equatorial OH groups of the cyclitol ring of the inositol to calcium at the carbohydrate binding site. Myoinositol binding occurred in two major orientations, while inositol 1-phosphate appeared primarily constrained to a single, different orientation. Our studies directly implicate the CRD in PI binding and reveal unexpected species differences in PI recognition that can be largely attributed to the side chain of residue 343. In addition, the studies indicate that oligomerization of trimeric subunits is an important determinant of recognition of PI by human SP-D.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
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.