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PDBsum entry 1uzx
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Transport protein PDB id
1uzx

 

 

 

 

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Contents
Protein chains
141 a.a. *
75 a.a. *
Ligands
MES
SO4
Waters ×126
* Residue conservation analysis
PDB id:
1uzx
Name: Transport protein
Title: A complex of the vps23 uev with ubiquitin
Structure: Vacuolar protein sorting-associated protein vps23. Chain: a. Fragment: uev domain, residues 1-161. Synonym: vps23, stp22. Engineered: yes. Ubiquitin. Chain: b
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3. Bos taurus. Bovine. Organism_taxid: 9913
Biol. unit: Dimer (from PDB file)
Resolution:
1.85Å     R-factor:   0.241     R-free:   0.274
Authors: H.Teo,R.L.Williams
Key ref:
H.Teo et al. (2004). Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins. J Biol Chem, 279, 28689-28696. PubMed id: 15044434 DOI: 10.1074/jbc.M400023200
Date:
18-Mar-04     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25604  (STP22_YEAST) -  Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		385 a.a.
141 a.a.*
Protein chain
Pfam   ArchSchema ?
P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		690 a.a.
75 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1074/jbc.M400023200 J Biol Chem 279:28689-28696 (2004)
PubMed id: 15044434  
 
 
Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins.
H.Teo, D.B.Veprintsev, R.L.Williams.
 
  ABSTRACT  
 
The endosomal sorting complex required for transport (ESCRT-I) is a 350-kDa complex of three proteins, Vps23, Vps28, and Vps37. The N-terminal ubiquitin-conjugating enzyme E2 variant (UEV) domain of Vps23 is required for sorting ubiquitinated proteins into the internal vesicles of multivesicular bodies. UEVs are homologous to E2 ubiquitin ligases but lack the conserved cysteine residue required for catalytic activity. The crystal structure of the yeast Vps23 UEV in a complex with ubiquitin (Ub) shows the detailed interactions made with the bound Ub. Compared with the solution structure of the Tsg101 UEV (the human homologue of Vps23) in the absence of Ub, two loops that are conserved among the ESCRT-I UEVs move toward each other to grip the Ub in a pincer-like grasp. The contacts with the UEV encompass two adjacent patches on the surface of the Ub, one containing several hydrophobic residues, including Ile-8(Ub), Ile-44(Ub), and Val-70(Ub), and the second containing a hydrophilic patch including residues Asn-60(Ub), Gln-62(Ub), Glu-64(Ub). The hydrophobic Ub patch interacting with the Vps23 UEV overlaps the surface of Ub interacting with the Vps27 ubiquitin-interacting motif, suggesting a sequential model for ubiquitinated cargo binding by these proteins. In contrast, the hydrophilic patch encompasses residues uniquely interacting with the ESCRT-I UEV. The structure provides a detailed framework for design of mutants that can specifically affect ESCRT-I-dependent sorting of ubiquitinated cargo without affecting Vps27-mediated delivery of cargo to endosomes.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Stereo representation of the detailed interactions between the UEV and the bound Ub. Residues in direct contact (closer than 4.0 Å) between the Vps23 UEV (yellow) and the Ub (magenta) are labeled. Direct hydrogen bonds between the UEV and the Ub are indicated as dashed lines. 		Figure 6.
FIG. 6. A comparison of the yeast and human ESCRT-I UEVs. Left, representations of the Vps23 UEV/Ub complex; right, representations of the Tsg101 UEV complex with a PTAP-peptide from the HIV-1 p6 protein (65). The vestigial active-site loop is colored cyan and the -hairpin tongue and lip are colored red. The Ub bound to the Vps23 UEV is colored green, and the PTAP peptide bound to Tsg101 is colored black.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 28689-28696) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21432937 K.Y.Huang, G.A.Amodeo, L.Tong, and A.McDermott (2011).
The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch.
  Protein Sci, 20, 630-639.
PDB code: 3ons
20028738 A.Herrador, S.Herranz, D.Lara, and O.Vincent (2010).
Recruitment of the ESCRT machinery to a putative seven-transmembrane-domain receptor is mediated by an arrestin-related protein.
  Mol Cell Biol, 30, 897-907.  
20154706 A.R.Cole, L.P.Lewis, and H.Walden (2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
  Nat Struct Mol Biol, 17, 294-298.
PDB code: 3k1l
21158740 D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.
  Biochem J, 433, 31-42.  
20588296 J.H.Hurley, and P.I.Hanson (2010).
Membrane budding and scission by the ESCRT machinery: it's all in the neck.
  Nat Rev Mol Cell Biol, 11, 556-566.  
20653365 J.H.Hurley (2010).
The ESCRT complexes.
  Crit Rev Biochem Mol Biol, 45, 463-487.  
21179194 L.B.Kramer, J.Shim, M.L.Previtera, N.R.Isack, M.C.Lee, B.L.Firestein, and C.Rongo (2010).
UEV-1 is an ubiquitin-conjugating enzyme variant that regulates glutamate receptor trafficking in C. elegans neurons.
  PLoS One, 5, e14291.  
20399684 S.Vardhana, K.Choudhuri, R.Varma, and M.L.Dustin (2010).
Essential role of ubiquitin and TSG101 protein in formation and function of the central supramolecular activation cluster.
  Immunity, 32, 531-540.  
21070952 Y.J.Im, L.Kuo, X.Ren, P.V.Burgos, X.Z.Zhao, F.Liu, T.R.Burke, J.S.Bonifacino, E.O.Freed, and J.H.Hurley (2010).
Crystallographic and functional analysis of the ESCRT-I /HIV-1 Gag PTAP interaction.
  Structure, 18, 1536-1547.
PDB codes: 3obq 3obs 3obu 3obx
19535732 B.McDonald, and J.Martin-Serrano (2009).
No strings attached: the ESCRT machinery in viral budding and cytokinesis.
  J Cell Sci, 122, 2167-2177.  
19008921 C.M.Fader, and M.I.Colombo (2009).
Autophagy and multivesicular bodies: two closely related partners.
  Cell Death Differ, 16, 70-78.  
19578117 J.Hol, A.M.Küchler, F.E.Johansen, B.Dalhus, G.Haraldsen, and I.Oynebråten (2009).
Molecular requirements for sorting of the chemokine interleukin-8/CXCL8 to endothelial Weibel-Palade bodies.
  J Biol Chem, 284, 23532-23539.  
19380877 S.B.Shields, A.J.Oestreich, S.Winistorfer, D.Nguyen, J.A.Payne, D.J.Katzmann, and R.Piper (2009).
ESCRT ubiquitin-binding domains function cooperatively during MVB cargo sorting.
  J Cell Biol, 185, 213-224.  
18284681 J.Brun, R.Chiu, K.Lockhart, W.Xiao, B.G.Wouters, and D.A.Gray (2008).
hMMS2 serves a redundant role in human PCNA polyubiquitination.
  BMC Mol Biol, 9, 24.  
18523727 N.A.Lakomek, K.F.Walter, C.Farès, O.F.Lange, B.L.de Groot, H.Grubmüller, R.Brüschweiler, A.Munk, S.Becker, J.Meiler, and C.Griesinger (2008).
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.
  J Biomol NMR, 41, 139-155.  
18429951 N.Tanaka, M.Kyuuma, and K.Sugamura (2008).
Endosomal sorting complex required for transport proteins in cancer pathogenesis, vesicular transport, and non-endosomal functions.
  Cancer Sci, 99, 1293-1303.  
17696968 A.Galindo, A.Hervás-Aguilar, O.Rodríguez-Galán, O.Vincent, H.N.Arst, J.Tilburn, and M.A.Peñalva (2007).
PalC, one of two Bro1 domain proteins in the fungal pH signalling pathway, localizes to cortical structures and binds Vps32.
  Traffic, 8, 1346-1364.  
17151358 A.J.Oestreich, B.A.Davies, J.A.Payne, and D.J.Katzmann (2007).
Mvb12 is a novel member of ESCRT-I involved in cargo selection by the multivesicular body pathway.
  Mol Biol Cell, 18, 646-657.  
  18005716 E.Morita, V.Sandrin, S.L.Alam, D.M.Eckert, S.P.Gygi, and W.I.Sundquist (2007).
Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding.
  Cell Host Microbe, 2, 41-53.  
17135292 M.Curtiss, C.Jones, and M.Babst (2007).
Efficient cargo sorting by ESCRT-I and the subsequent release of ESCRT-I from multivesicular bodies requires the subunit Mvb12.
  Mol Biol Cell, 18, 636-645.  
17442384 M.S.Kostelansky, C.Schluter, Y.Y.Tam, S.Lee, R.Ghirlando, B.Beach, E.Conibear, and J.H.Hurley (2007).
Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer.
  Cell, 129, 485-498.
PDB code: 2p22
17506697 R.C.Piper, and D.J.Katzmann (2007).
Biogenesis and function of multivesicular bodies.
  Annu Rev Cell Dev Biol, 23, 519-547.  
17450176 R.L.Williams, and S.Urbé (2007).
The emerging shape of the ESCRT machinery.
  Nat Rev Mol Cell Biol, 8, 355-368.  
16552148 A.Palencia, J.C.Martinez, P.L.Mateo, I.Luque, and A.Camara-Artigas (2006).
Structure of human TSG101 UEV domain.
  Acta Crystallogr D Biol Crystallogr, 62, 458-464.
PDB code: 2f0r
16749904 E.Pineda-Molina, H.Belrhali, A.J.Piefer, I.Akula, P.Bates, and W.Weissenhorn (2006).
The crystal structure of the C-terminal domain of Vps28 reveals a conserved surface required for Vps20 recruitment.
  Traffic, 7, 1007-1016.
PDB code: 2g3k
16615893 H.Teo, D.J.Gill, J.Sun, O.Perisic, D.B.Veprintsev, Y.Vallis, S.D.Emr, and R.L.Williams (2006).
ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes.
  Cell, 125, 99.
PDB codes: 2cay 2caz
16689637 J.H.Hurley, and S.D.Emr (2006).
The ESCRT complexes: structure and mechanism of a membrane-trafficking network.
  Annu Rev Biophys Biomol Struct, 35, 277-298.  
16781134 M.R.Russell, D.P.Nickerson, and G.Odorizzi (2006).
Molecular mechanisms of late endosome morphology, identity and sorting.
  Curr Opin Cell Biol, 18, 422-428.  
16615894 M.S.Kostelansky, J.Sun, S.Lee, J.Kim, R.Ghirlando, A.Hierro, S.D.Emr, and J.H.Hurley (2006).
Structural and functional organization of the ESCRT-I trafficking complex.
  Cell, 125, 113-126.
PDB codes: 2f66 2f6m
16428608 P.Bellare, A.K.Kutach, A.K.Rines, C.Guthrie, and E.J.Sontheimer (2006).
Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p.
  RNA, 12, 292-302.  
16462748 S.Hirano, M.Kawasaki, H.Ura, R.Kato, C.Raiborg, H.Stenmark, and S.Wakatsuki (2006).
Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting.
  Nat Struct Mol Biol, 13, 272-277.
PDB code: 2d3g
17057714 S.Hirano, N.Suzuki, T.Slagsvold, M.Kawasaki, D.Trambaiolo, R.Kato, H.Stenmark, and S.Wakatsuki (2006).
Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain.
  Nat Struct Mol Biol, 13, 1031-1032.
PDB code: 2dx5
17057716 S.L.Alam, C.Langelier, F.G.Whitby, S.Koirala, H.Robinson, C.P.Hill, and W.I.Sundquist (2006).
Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain.
  Nat Struct Mol Biol, 13, 1029-1030.
PDB code: 2hth
16518384 S.L.Alam, and W.I.Sundquist (2006).
Two new structures of Ub-receptor complexes. U2.
  Nat Struct Mol Biol, 13, 186-188.  
15837191 A.Ohno, J.Jee, K.Fujiwara, T.Tenno, N.Goda, H.Tochio, H.Kobayashi, H.Hiroaki, and M.Shirakawa (2005).
Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition.
  Structure, 13, 521-532.
PDB code: 1wr1
15694336 D.T.Huang, A.Paydar, M.Zhuang, M.B.Waddell, J.M.Holton, and B.A.Schulman (2005).
Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.
  Mol Cell, 17, 341-350.
PDB code: 1y8x
15701688 G.Prag, S.Lee, R.Mattera, C.N.Arighi, B.M.Beach, J.S.Bonifacino, and J.H.Hurley (2005).
Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins.
  Proc Natl Acad Sci U S A, 102, 2334-2339.
PDB code: 1yd8
15935782 J.Kim, S.Sitaraman, A.Hierro, B.M.Beach, G.Odorizzi, and J.H.Hurley (2005).
Structural basis for endosomal targeting by the Bro1 domain.
  Dev Cell, 8, 937-947.
PDB code: 1zb1
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
15966896 M.Kawasaki, T.Shiba, Y.Shiba, Y.Yamaguchi, N.Matsugaki, N.Igarashi, M.Suzuki, R.Kato, K.Kato, K.Nakayama, and S.Wakatsuki (2005).
Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.
  Genes Cells, 10, 639-654.
PDB code: 1wr6
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.

 

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