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protein Protein-protein interface(s) links
Cytokine PDB id
1gif
Jmol
Contents
Protein chains
115 a.a. *
Waters ×170
* Residue conservation analysis
PDB id:
1gif
Name: Cytokine
Title: Human glycosylation-inhibiting factor
Structure: Glycosylation-inhibiting factor. Chain: a, b, c. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
1.90Å     R-factor:   0.168    
Authors: Y.Kato,R.Kuroki
Key ref: Y.Kato et al. (1996). The crystal structure of human glycosylation-inhibiting factor is a trimeric barrel with three 6-stranded beta-sheets. Proc Natl Acad Sci U S A, 93, 3007-3010. PubMed id: 8610159
Date:
27-Feb-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14174  (MIF_HUMAN) -  Macrophage migration inhibitory factor
Seq:
Struc:
115 a.a.
115 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.5.3.2.1  - Phenylpyruvate tautomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Keto-phenylpyruvate = enol-phenylpyruvate
Keto-phenylpyruvate
= enol-phenylpyruvate
   Enzyme class 3: E.C.5.3.3.12  - L-dopachrome isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate
L-dopachrome
= 5,6-dihydroxyindole-2-carboxylate
      Cofactor: Zn(2+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   5 terms 
  Biological process     immune system process   37 terms 
  Biochemical function     chemoattractant activity     8 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 93:3007-3010 (1996)
PubMed id: 8610159  
 
 
The crystal structure of human glycosylation-inhibiting factor is a trimeric barrel with three 6-stranded beta-sheets.
Y.Kato, T.Muto, T.Tomura, H.Tsumura, H.Watarai, T.Mikayama, K.Ishizaka, R.Kuroki.
 
  ABSTRACT  
 
Glycosylation-inhibiting factor (GIF) is a cytokine that is involved in the regulation of IgE synthesis. The crystal structure of recombinant human GIF was determined by the multiple isomorphous replacement method. The structure was refined to an R factor of 0.168 at 1.9 angstrom resolution. The overall structure is seen to consist of three interconnected subunits forming a barrel with three 6-stranded beta-sheets on the inside and six alpha-helices on the outside. There is a 5-angstrom-diameter "hole" through the middle of the barrel. The barrel structure of GIF in part resembles other "trefoil" cytokines such as interleukin 1 and fibroblast growth factor. Each subunit has a new class of alpha + beta sandwich structure consisting of two beta-alpha-beta motifs. These beta-alpha-beta motifs are related by a pseudo-twofold axis and resemble both interleukin 8 and the peptide binding domain of major histocompatibility complex protein, although the topology of the polypeptide chain is quite different.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19601712 A.Son, N.Kato, T.Horibe, Y.Matsuo, M.Mochizuki, A.Mitsui, K.Kawakami, H.Nakamura, and J.Yodoi (2009).
Direct association of thioredoxin-1 (TRX) with macrophage migration inhibitory factor (MIF): regulatory role of TRX on MIF internalization and signaling.
  Antioxid Redox Signal, 11, 2595-2605.  
16474429 L.Leng, and R.Bucala (2006).
Insight into the biology of macrophage migration inhibitory factor (MIF) revealed by the cloning of its cell surface receptor.
  Cell Res, 16, 162-168.  
11069294 H.Watarai, R.Nozawa, A.Tokunaga, N.Yuyama, M.Tomas, A.Hinohara, K.Ishizaka, and Y.Ishii (2000).
Posttranslational modification of the glycosylation inhibiting factor (GIF) gene product generates bioactive GIF.
  Proc Natl Acad Sci U S A, 97, 13251-13256.  
10215893 R.Kleemann, A.Kapurniotu, R.Mischke, J.Held, and J.Bernhagen (1999).
Characterization of catalytic centre mutants of macrophage migration inhibitory factor (MIF) and comparison to Cys81Ser MIF.
  Eur J Biochem, 261, 753-766.  
9640239 C.C.Wang, and G.A.Rook (1998).
Inhibition of an established allergic response to ovalbumin in BALB/c mice by killed Mycobacterium vaccae.
  Immunology, 93, 307-313.  
9649424 M.Swope, H.W.Sun, P.R.Blake, and E.Lolis (1998).
Direct link between cytokine activity and a catalytic site for macrophage migration inhibitory factor.
  EMBO J, 17, 3534-3541.  
9629239 R.Bucala (1998).
Neuroimmunomodulation by macrophage migration inhibitory factor (MIF).
  Ann N Y Acad Sci, 840, 74-82.  
9266180 E.Gouaux (1997).
Channel-forming toxins: tales of transformation.
  Curr Opin Struct Biol, 7, 566-573.  
9144228 K.Sugie, T.Nakano, T.Tomura, K.Takakura, T.Mikayama, and K.Ishizaka (1997).
High-affinity binding of bioactive glycosylation-inhibiting factor to antigen-primed T cells and natural killer cells.
  Proc Natl Acad Sci U S A, 94, 5278-5283.  
8990186 T.Nakano, H.Watarai, Y.C.Liu, Y.Oyama, T.Mikayama, and K.Ishizaka (1997).
Conversion of inactive glycosylation inhibiting factor to bioactive derivatives by modification of a SH group.
  Proc Natl Acad Sci U S A, 94, 202-207.  
8804825 A.G.Murzin (1996).
Structural classification of proteins: new superfamilies.
  Curr Opin Struct Biol, 6, 386-394.  
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.