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PDBsum entry 1umi

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Ligase PDB id
1umi
Jmol
Contents
Protein chain
184 a.a. *
Ligands
NDG-NAG
Waters ×45
* Residue conservation analysis
PDB id:
1umi
Name: Ligase
Title: Structural basis of sugar-recognizing ubiquitin ligase
Structure: F-box only protein 2. Chain: a. Fragment: sbd domain. Synonym: fbs1. Engineered: yes. Mutation: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: mouse. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.200     R-free:   0.256
Authors: T.Mizushima,T.Hirao,Y.Yoshida,S.J.Lee,T.Chiba,K.Iwai,Y.Yamag K.Kato,T.Tsukihara,K.Tanaka
Key ref:
T.Mizushima et al. (2004). Structural basis of sugar-recognizing ubiquitin ligase. Nat Struct Mol Biol, 11, 365-370. PubMed id: 14990996 DOI: 10.1038/nsmb732
Date:
01-Oct-03     Release date:   06-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q80UW2  (FBX2_MOUSE) -  F-box only protein 2
Seq:
Struc:
297 a.a.
184 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein catabolic process   1 term 

 

 
DOI no: 10.1038/nsmb732 Nat Struct Mol Biol 11:365-370 (2004)
PubMed id: 14990996  
 
 
Structural basis of sugar-recognizing ubiquitin ligase.
T.Mizushima, T.Hirao, Y.Yoshida, S.J.Lee, T.Chiba, K.Iwai, Y.Yamaguchi, K.Kato, T.Tsukihara, K.Tanaka.
 
  ABSTRACT  
 
SCF(Fbs1) is a ubiquitin ligase that functions in the endoplasmic reticulum (ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins, recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose). Here we report the crystal structures of the sugar-binding domain (SBD) of Fbs1 alone and in complex with chitobiose. The SBD is composed of a ten-stranded antiparallel beta-sandwich. The structure of the SBD-chitobiose complex includes hydrogen bonds between Fbs1 and chitobiose and insertion of the methyl group of chitobiose into a small hydrophobic pocket of Fbs1. Moreover, NMR spectroscopy has demonstrated that the amino acid residues adjoining the chitobiose-binding site interact with the outer branches of the carbohydrate moiety. Considering that the innermost chitobiose moieties in N-glycans are usually involved in intramolecular interactions with the polypeptide moieties, we propose that Fbs1 interacts with the chitobiose in unfolded N-glycoprotein, pointing the protein moiety toward E2 for ubiquitination.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Tertiary structure of SBD in Fbs1. (a) Overall structure of SBD of Fbs1 shown as a ribbon diagram. -strands belonging to S1 and S2 are blue and red, respectively. Loops and helices are black and yellow, respectively. (b) A topology diagram of SBD. The -helices are yellow cylinders labeled 1 and 2. The -strands are arrows labeled 1 - 10. The left and right forms of -strands correspond to S1 and S2, respectively, as in a. N and C, N and C termini, respectively. (c) Amino acid sequences of SBD in Fbs1 and corresponding region of Fbs2. Amino acid residues are numbered in the N-to-C direction, for example, from position 117 to position 297 (C-terminal end) of Fbs1, and from 69 to 295 (C-terminal end) of Fbs2. Identical residues are boxed. Secondary structure elements are colored as a. Substrate-binding residues are red characters.
Figure 2.
Figure 2. Structure of SBD in complex with chitobiose. (a) Stereo view of the difference-density map (F[o] - F[c] with phase from the Fbs1 model) of binding chitobiose, contoured at 2.1 , modeled into the electron density. -strands belonging to S1 and S2 are blue and red, respectively. Loops are black. The bound chitobiose is orange, and the residues involved in the substrate binding (FYWK, see Fig. 1c) are green. (b) Molecular surface representation of the chitobiose-binding region. The bound chitobiose is shown in ball-and-stick representation. Two GlcNAc residues are represented by A and B. Cyan spheres are two water molecules of wild type SBD that are fixed on the molecular surface through hydrogen bonds with the backbone N and O of Lys281, respectively. These water molecules are replaced by O3 and O6 of the chitobiose upon formation of the SBD -chitobiose complex. (c) Stick representation of the amino acids involved in binding. Hydrogen bonds are dashed lines. Oxygen and nitrogen are red and blue, respectively. Symbols of two water molecules are as in b.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 365-370) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21554755 A.Sarikas, T.Hartmann, and Z.Q.Pan (2011).
The cullin protein family.
  Genome Biol, 12, 220.  
21288713 D.M.Duda, D.C.Scott, M.F.Calabrese, E.S.Zimmerman, N.Zheng, and B.A.Schulman (2011).
Structural regulation of cullin-RING ubiquitin ligase complexes.
  Curr Opin Struct Biol, 21, 257-264.  
20854419 B.Gong, F.Chen, Y.Pan, I.Arrieta-Cruz, Y.Yoshida, V.Haroutunian, and G.M.Pasinetti (2010).
SCFFbx2-E3-ligase-mediated degradation of BACE1 attenuates Alzheimer's disease amyloidosis and improves synaptic function.
  Aging Cell, 9, 1018-1031.  
20466650 T.Schallus, K.Fehér, U.Sternberg, V.Rybin, and C.Muhle-Goll (2010).
Analysis of the specific interactions between the lectin domain of malectin and diglucosides.
  Glycobiology, 20, 1010-1020.
PDB code: 2kr2
18025086 B.Bae, S.Ohene-Adjei, S.Kocherginskaya, R.I.Mackie, M.A.Spies, I.K.Cann, and S.K.Nair (2008).
Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA.
  J Biol Chem, 283, 12415-12425.
PDB codes: 2zew 2zex 2zey 2zez
18203720 K.A.Glenn, R.F.Nelson, H.M.Wen, A.J.Mallinger, and H.L.Paulson (2008).
Diversity in tissue expression, substrate binding, and SCF complex formation for a lectin family of ubiquitin ligases.
  J Biol Chem, 283, 12717-12729.  
18698327 T.Ravid, and M.Hochstrasser (2008).
Diversity of degradation signals in the ubiquitin-proteasome system.
  Nat Rev Mol Cell Biol, 9, 679-690.  
18524852 T.Schallus, C.Jaeckh, K.Fehér, A.S.Palma, Y.Liu, J.C.Simpson, M.Mackeen, G.Stier, T.J.Gibson, T.Feizi, T.Pieler, and C.Muhle-Goll (2008).
Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation.
  Mol Biol Cell, 19, 3404-3414.
PDB codes: 2jwp 2k46
17477837 B.T.Dye, and B.A.Schulman (2007).
Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins.
  Annu Rev Biophys Biomol Struct, 36, 131-150.  
17389369 T.Mizushima, Y.Yoshida, T.Kumanomidou, Y.Hasegawa, A.Suzuki, T.Yamane, and K.Tanaka (2007).
Structural basis for the selection of glycosylated substrates by SCF(Fbs1) ubiquitin ligase.
  Proc Natl Acad Sci U S A, 104, 5777-5781.
PDB codes: 2e31 2e32 2e33
17215248 Y.Yoshida, A.Murakami, K.Iwai, and K.Tanaka (2007).
A neural-specific F-box protein Fbs1 functions as a chaperone suppressing glycoprotein aggregation.
  J Biol Chem, 282, 7137-7144.  
17986767 Y.Yoshida (2007).
F-box proteins that contain sugar-binding domains.
  Biosci Biotechnol Biochem, 71, 2623-2631.  
16682404 R.F.Nelson, K.A.Glenn, V.M.Miller, H.Wen, and H.L.Paulson (2006).
A novel route for F-box protein-mediated ubiquitination links CHIP to glycoprotein quality control.
  J Biol Chem, 281, 20242-20251.  
17088551 X.Zhou, G.Zhao, J.J.Truglio, L.Wang, G.Li, W.J.Lennarz, and H.Schindelin (2006).
Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module.
  Proc Natl Acad Sci U S A, 103, 17214-17219.
PDB codes: 2g9f 2g9g 2i74
16154739 Y.Ito, S.Hagihara, I.Matsuo, and K.Totani (2005).
Structural approaches to the study of oligosaccharides in glycoprotein quality control.
  Curr Opin Struct Biol, 15, 481-489.  
16129679 Y.Kamiya, Y.Yamaguchi, N.Takahashi, Y.Arata, K.Kasai, Y.Ihara, I.Matsuo, Y.Ito, K.Yamamoto, and K.Kato (2005).
Sugar-binding properties of VIP36, an intracellular animal lectin operating as a cargo receptor.
  J Biol Chem, 280, 37178-37182.  
15723043 Y.Yoshida, E.Adachi, K.Fukiya, K.Iwai, and K.Tanaka (2005).
Glycoprotein-specific ubiquitin ligases recognize N-glycans in unfolded substrates.
  EMBO Rep, 6, 239-244.  
15340381 T.Cardozo, and M.Pagano (2004).
The SCF ubiquitin ligase: insights into a molecular machine.
  Nat Rev Mol Cell Biol, 5, 739-751.  
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 code is shown on the right.