PDBsum entry 1y02

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protein metals links
Metal binding protein PDB id
Protein chain
91 a.a. *
_ZN ×2
Waters ×153
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Crystal structure of a fyve-type domain from caspase regulator carp2
Structure: Fyve-ring finger protein sakura. Chain: a. Fragment: carp2 fragment (residues 26-145). Synonym: carp2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.80Å     R-factor:   0.206     R-free:   0.234
Authors: M.D.Tibbetts,L.Gu,E.N.Shiozaki,Y.Shi
Key ref:
M.D.Tibbetts et al. (2004). Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2. Structure, 12, 2257-2263. PubMed id: 15576038 DOI: 10.1016/j.str.2004.10.007
14-Nov-04     Release date:   28-Dec-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8WZ73  (RFFL_HUMAN) -  E3 ubiquitin-protein ligase rififylin
363 a.a.
91 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure


DOI no: 10.1016/j.str.2004.10.007 Structure 12:2257-2263 (2004)
PubMed id: 15576038  
Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2.
M.D.Tibbetts, E.N.Shiozaki, L.Gu, E.R.McDonald, W.S.El-Deiry, Y.Shi.
The caspase-associated ring proteins (CARP1 and CARP2) are distinguished from other caspase regulators by the presence of a FYVE-type zinc finger domain. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function. Here, we report the crystal structure of the N-terminal region of CARP2 (44-139) including the FYVE-type domain and its associated helical bundle at 1.7 A resolution. The structure reveals a cramped phosphoinositide binding pocket and a blunted membrane insertion loop. These structural features indicate that the domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. The CARP2 FYVE-like domain thus defines a third subfamily of FYVE-type domains that are functionally and structurally distinct. Structural analyses provide insights into the possible function of this unique subfamily of FYVE-type domains.
  Selected figure(s)  
Figure 2.
Figure 2. The CARP2 FYVE-Type Domain Has Several Unique Structural Features(A) Comparison of the CARP2 FYVE-type domain with the EEA1 FYVE domain and the Rabphilin-3A FYVE-related domain. Several distinguishing structural features are highlighted, including the phosphoinositide binding pocket for EEA1, the b3-b4 loop, the membrane insertion tip, and the distinct kink in the loop close to the binding pocket in CARP2. Details of the membrane insertion region of all three proteins are shown in the inset. The CARP2 tip region lacks the hydrophobic property that is conserved in EEA1 and Rabphilin-3A.(B) A stereo view of the membrane insertion loop of CARP2. The 2Fo-Fc electron density map, colored magenta and contoured at 1.2 s, is shown at the tip of membrane insert loop. The three amino acid residues at the tip, Ala55, Asn56, and Thr57, are labeled.(C) Sequence alignment of the FYVE-type domains from CARP2, CARP1, Fgd1, Vps27p, Hrs, EEA1, SARA, Rabphilin-3A, and NOC2. The alignment highlights the conservation of the zinc-coordinating cysteines and key sequence differences between the different subfamilies of FYVE-type domains. Note that the WxxD motif is conserved only in phosphoinositide binding FYVE domains. The solid line identifies the R(R/K)HHCR signature motif, and the double line indicates the C-terminal RVC motif. The membrane insertion tip residues are indicated by a wavy line. The eight conserved cysteines that coordinate two zinc atoms are indicated with asterisks. The conserved glycine in FYVE domains is indicated by a yellow box, and the conserved glycine in FYVE-related domains is indicated by a blue triangle.
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 2257-2263) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18450452 W.Liao, Q.Xiao, V.Tchikov, K.Fujita, W.Yang, S.Wincovitch, S.Garfield, D.Conze, W.S.El-Deiry, S.Schütze, and S.M.Srinivasula (2008).
CARP-2 is an endosome-associated ubiquitin ligase for RIP and regulates TNF-induced NF-kappaB activation.
  Curr Biol, 18, 641-649.  
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