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PDBsum entry 1dfv
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protein ligands Protein-protein interface(s) links
Sugar binding protein PDB id
1dfv

 

 

 

 

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Contents
Protein chain
173 a.a. *
Ligands
NAG-NAG
SO4 ×3
NAG
Waters ×133
* Residue conservation analysis
PDB id:
1dfv
Name: Sugar binding protein
Title: Crystal structure of human neutrophil gelatinase associated lipocalin monomer
Structure: Human neutrophil gelatinase. Chain: a, b. Synonym: ngal. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: unidentified baculovirus. Expression_system_taxid: 10469
Resolution:
2.60Å     R-factor:   0.281     R-free:   0.293
Authors: D.H.Goetz,S.T.Willie,R.S.Armen,T.Bratt,N.Borregaard,R.K.Strong
Key ref:
D.H.Goetz et al. (2000). Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin. Biochemistry, 39, 1935-1941. PubMed id: 10684642 DOI: 10.1021/bi992215v
Date:
22-Nov-99     Release date:   06-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80188  (NGAL_HUMAN) -  Neutrophil gelatinase-associated lipocalin from Homo sapiens
Seq:
Struc: 		198 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi992215v Biochemistry 39:1935-1941 (2000)
PubMed id: 10684642  
 
 
Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin.
D.H.Goetz, S.T.Willie, R.S.Armen, T.Bratt, N.Borregaard, R.K.Strong.
 
  ABSTRACT  
 
Neutrophil gelatinase associated lipocalin (NGAL), a constituent of neutrophil granules, is a member of the lipocalin family of binding proteins. NGAL can also be highly induced in epithelial cells in both inflammatory and neoplastic colorectal disease. NGAL is proposed to mediate inflammatory responses by sequestering neutrophil chemoattractants, particularly N-formylated tripeptides and possibly leukotriene B(4) and platelet activating factor. The crystal structures of NGAL display a typical lipocalin fold, albeit with an unusually large and atypically polar binding site, or calyx. The fold of NGAL is most similar to the epididymal retinoic acid-binding protein, another lipocalin, though the overall architecture of the calyces are very different. The crystal structures also reveal either sulfate ions or an adventitiously copurified fatty acid bound in the binding site. Neither ligand is displaced by added N-formylated tripeptides. The size, shape, and character of the NGAL calyx, as well as the low relative affinity for N-formylated tripeptides, suggest that neither the copurified fatty acid nor any of the proposed ligands are likely to be the preferred ligand of this protein. Comparisons between the crystal structures and the recently reported solution structure of NGAL reveal significant differences, in terms of both the details of the structure and the overall flexibility of the fold.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21439274 H.T.Tsai, P.H.Su, T.H.Lee, Y.T.Tee, L.Y.Lin, S.F.Yang, and P.H.Wang (2011).
Significant elevation and correlation of plasma neutrophil gelatinase associated lipocalin and its complex with matrix metalloproteinase-9 in patients with pelvic inflammatory disease.
  Clin Chim Acta, 412, 1252-1256.  
20581821 G.Bao, M.Clifton, T.M.Hoette, K.Mori, S.X.Deng, A.Qiu, M.Viltard, D.Williams, N.Paragas, T.Leete, R.Kulkarni, X.Li, B.Lee, A.Kalandadze, A.J.Ratner, J.C.Pizarro, K.M.Schmidt-Ott, D.W.Landry, K.N.Raymond, R.K.Strong, and J.Barasch (2010).
Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.
  Nat Chem Biol, 6, 602-609.
PDB codes: 3fw4 3fw5
19949414 J.M.Moreno-Navarrete, M.Manco, J.Ibáñez, E.García-Fuentes, F.Ortega, E.Gorostiaga, J.Vendrell, M.Izquierdo, C.Martínez, G.Nolfe, W.Ricart, G.Mingrone, F.Tinahones, and J.M.Fernández-Real (2010).
Metabolic endotoxemia and saturated fat contribute to circulating NGAL concentrations in subjects with insulin resistance.
  Int J Obes (Lond), 34, 240-249.  
19770509 D.A.Breustedt, L.Chatwell, and A.Skerra (2009).
A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity.
  Acta Crystallogr D Biol Crystallogr, 65, 1118-1125.
PDB code: 3eyc
  18720059 H.J.Woo, J.C.Park, C.H.Bae, S.Y.Song, H.M.Lee, and Y.D.Kim (2009).
Up-regulation of neutrophil gelatinase-associated lipocalin in cholesteatoma.
  Acta Otolaryngol, 129, 624-629.  
19184458 M.C.Clifton, C.Corrent, and R.K.Strong (2009).
Siderocalins: siderophore-binding proteins of the innate immune system.
  Biometals, 22, 557-564.  
19772347 M.Sandy, and A.Butler (2009).
Microbial iron acquisition: marine and terrestrial siderophores.
  Chem Rev, 109, 4580-4595.  
19342674 Y.R.Chan, J.S.Liu, D.A.Pociask, M.Zheng, T.A.Mietzner, T.Berger, T.W.Mak, M.C.Clifton, R.K.Strong, P.Ray, and J.K.Kolls (2009).
Lipocalin 2 is required for pulmonary host defense against Klebsiella infection.
  J Immunol, 182, 4947-4956.  
18725016 D.Bolignano, V.Donato, G.Coppolino, S.Campo, A.Buemi, A.Lacquaniti, and M.Buemi (2008).
Neutrophil gelatinase-associated lipocalin (NGAL) as a marker of kidney damage.
  Am J Kidney Dis, 52, 595-605.  
18974761 F.Wei, A.Karihaloo, Z.Yu, A.Marlier, P.Seth, S.Shibazaki, T.Wang, V.P.Sukhatme, S.Somlo, and L.G.Cantley (2008).
Neutrophil gelatinase-associated lipocalin suppresses cyst growth by Pkd1 null cells in vitro and in vivo.
  Kidney Int, 74, 1310-1318.  
18437016 J.H.Lee, K.C.Kye, E.Y.Seo, K.Lee, S.K.Lee, J.S.Lim, Y.J.Seo, C.D.Kim, and J.K.Park (2008).
Expression of neutrophil gelatinase-associated lipocalin in calcium-induced keratinocyte differentiation.
  J Korean Med Sci, 23, 302-306.  
17391123 F.Aigner, H.T.Maier, H.G.Schwelberger, E.A.Wallnöfer, A.Amberger, P.Obrist, T.Berger, T.W.Mak, M.Maglione, R.Margreiter, S.Schneeberger, and J.Troppmair (2007).
Lipocalin-2 regulates the inflammatory response during ischemia and reperfusion of the transplanted heart.
  Am J Transplant, 7, 779-788.  
17060628 M.A.Fischbach, H.Lin, L.Zhou, Y.Yu, R.J.Abergel, D.R.Liu, K.N.Raymond, B.L.Wanner, R.K.Strong, C.T.Walsh, A.Aderem, and K.D.Smith (2006).
The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2.
  Proc Natl Acad Sci U S A, 103, 16502-16507.  
16718606 N.Borregaard, and J.B.Cowland (2006).
Neutrophil gelatinase-associated lipocalin, a siderophore-binding eukaryotic protein.
  Biometals, 19, 211-215.  
16952550 R.J.Playford, A.Belo, R.Poulsom, A.J.Fitzgerald, K.Harris, I.Pawluczyk, J.Ryon, T.Darby, M.Nilsen-Hamilton, S.Ghosh, and T.Marchbank (2006).
Effects of mouse and human lipocalin homologues 24p3/lcn2 and neutrophil gelatinase-associated lipocalin on gastrointestinal mucosal integrity and repair.
  Gastroenterology, 131, 809-817.  
15489503 D.A.Breustedt, I.P.Korndörfer, B.Redl, and A.Skerra (2005).
The 1.8-A crystal structure of human tear lipocalin reveals an extended branched cavity with capacity for multiple ligands.
  J Biol Chem, 280, 484-493.
PDB code: 1xki
15637066 J.A.Gwira, F.Wei, S.Ishibe, J.M.Ueland, J.Barasch, and L.G.Cantley (2005).
Expression of neutrophil gelatinase-associated lipocalin regulates epithelial morphogenesis in vitro.
  J Biol Chem, 280, 7875-7882.  
15642259 M.A.Holmes, W.Paulsene, X.Jide, C.Ratledge, and R.K.Strong (2005).
Siderocalin (Lcn 2) also binds carboxymycobactins, potentially defending against mycobacterial infections through iron sequestration.
  Structure, 13, 29-41.
PDB codes: 1x71 1x89 1x8u
15802951 N.K.Krishna (2005).
Identification of structural domains involved in astrovirus capsid biology.
  Viral Immunol, 18, 17-26.  
16255649 S.Schlehuber, and A.Skerra (2005).
Anticalins as an alternative to antibody technology.
  Expert Opin Biol Ther, 5, 1453-1462.  
  15331587 C.E.Doneanu, R.K.Strong, and W.N.Howald (2004).
Characterization of a noncovalent lipocalin complex by liquid chromatography/electrospray ionization mass spectrometry.
  J Biomol Tech, 15, 208-212.  
15316916 H.Oku, T.Ohyama, A.Hiroki, K.Yamada, K.Fukuyama, H.Kawaguchi, and R.Katakai (2004).
Addition of a peptide fragment on an alpha-helical depsipeptide induces alpha/3(10)-conjugated helix: synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt.
  Biopolymers, 75, 242-254.  
12655062 K.N.Raymond, E.A.Dertz, and S.S.Kim (2003).
Enterobactin: an archetype for microbial iron transport.
  Proc Natl Acad Sci U S A, 100, 3584-3588.  
12453412 D.H.Goetz, M.A.Holmes, N.Borregaard, M.E.Bluhm, K.N.Raymond, and R.K.Strong (2002).
The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition.
  Mol Cell, 10, 1033-1043.
PDB code: 1l6m
12473066 L.Mallbris, K.P.O'Brien, A.Hulthén, B.Sandstedt, J.B.Cowland, N.Borregaard, and M.Ståhle-Bäckdahl (2002).
Neutrophil gelatinase-associated lipocalin is a marker for dysregulated keratinocyte differentiation in human skin.
  Exp Dermatol, 11, 584-591.  
11277914 H.Tschesche, V.Zölzer, S.Triebel, and S.Bartsch (2001).
The human neutrophil lipocalin supports the allosteric activation of matrix metalloproteinases.
  Eur J Biochem, 268, 1918-1928.  
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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