PDBsum entry 1p98

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protein links
Replication PDB id
Jmol PyMol
Protein chain
78 a.a. *
* Residue conservation analysis
PDB id:
Name: Replication
Title: High-resolution nmr structure of the ubl-domain of hhr23a
Structure: Uv excision repair protein rad23 homolog a. Chain: a. Fragment: ubiquitin-like domain. Synonym: hhr23a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rad23a. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 11 models
Authors: T.D.Mueller,J.Feigon
Key ref: T.D.Mueller and J.Feigon (2003). Structural determinants for the binding of ubiquitin-like domains to the proteasome. EMBO J, 22, 4634-4645. PubMed id: 12970176
09-May-03     Release date:   07-Oct-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P54725  (RD23A_HUMAN) -  UV excision repair protein RAD23 homolog A
363 a.a.
78 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


EMBO J 22:4634-4645 (2003)
PubMed id: 12970176  
Structural determinants for the binding of ubiquitin-like domains to the proteasome.
T.D.Mueller, J.Feigon.
HHR23A, a protein implicated in nucleotide excision repair, belongs to a class of proteins containing both a ubiquitin-like (Ubl) domain and one or more ubiquitin-associated (UBA) domains, suggesting a role in the ubiquitin-proteasome pathway as well. The Ubl domain binds with high affinity to the second ubiquitin-interacting motif (UIM) of the S5a subunit of the proteasome. Here we present the solution structures of the HHR23A Ubl domain, the second UIM of S5a (UIM-2), and the Ubl:S5a-UIM-2 complex. The HHR23A Ubl domain is structurally similar to ubiquitin. The S5a UIM forms an alpha-helix with an unexpected hairpin loop that contributes to the binding interface with Ubl. The molecular determinants of the Ubl-proteasome interaction are revealed by analysis of the structures, chemical shift mapping, mutant binding studies and sequence conservation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21348451 S.S.Safadi, K.R.Barber, and G.S.Shaw (2011).
Impact of autosomal recessive juvenile Parkinson's disease mutations on the structure and interactions of the parkin ubiquitin-like domain.
  Biochemistry, 50, 2603-2610.  
21047872 Y.W.Chen, T.Tajima, and S.Agrawal (2011).
The crystal structure of the ubiquitin-like (UbL) domain of human homologue A of Rad23 (hHR23A) protein.
  Protein Eng Des Sel, 24, 131-138.
PDB code: 2wyq
20949063 A.X.Song, C.J.Zhou, Y.Peng, X.C.Gao, Z.R.Zhou, Q.S.Fu, J.Hong, D.H.Lin, and H.Y.Hu (2010).
Structural transformation of the tandem ubiquitin-interacting motifs in ataxin-3 and their cooperative interactions with ubiquitin chains.
  PLoS One, 5, e13202.  
20053359 N.G.Sgourakis, M.M.Patel, A.E.Garcia, G.I.Makhatadze, and S.A.McCallum (2010).
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
  J Mol Biol, 396, 1128-1144.
PDB code: 2kdi
19875440 S.S.Safadi, and G.S.Shaw (2010).
Differential interaction of the E3 ligase parkin with the proteasomal subunit S5a and the endocytic protein Eps15.
  J Biol Chem, 285, 1424-1434.  
20064467 D.Zhang, T.Chen, I.Ziv, R.Rosenzweig, Y.Matiuhin, V.Bronner, M.H.Glickman, and D.Fushman (2009).
Together, Rpn10 and Dsk2 can serve as a polyubiquitin chain-length sensor.
  Mol Cell, 36, 1018-1033.  
19796170 N.Yoshimoto, K.Tatematsu, T.Okajima, K.Tanizawa, and S.Kuroda (2009).
Accumulation of polyubiquitinated proteins by overexpression of RBCC protein interacting with protein kinase C2, a splice variant of ubiquitin ligase RBCC protein interacting with protein kinase C1.
  FEBS J, 276, 6375-6385.  
19468686 V.Su, and A.F.Lau (2009).
Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation.
  Cell Mol Life Sci, 66, 2819-2833.  
18079109 X.Li, V.Su, W.E.Kurata, C.Jin, and A.F.Lau (2008).
A novel connexin43-interacting protein, CIP75, which belongs to the UbL-UBA protein family, regulates the turnover of connexin43.
  J Biol Chem, 283, 5748-5759.  
18083189 Y.C.Kim, and G.Hummer (2008).
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
  J Mol Biol, 375, 1416-1433.  
17368669 A.Haririnia, M.D'Onofrio, and D.Fushman (2007).
Mapping the interactions between Lys48 and Lys63-linked di-ubiquitins and a ubiquitin-interacting motif of S5a.
  J Mol Biol, 368, 753-766.  
17646385 J.Hamazaki, K.Sasaki, H.Kawahara, S.Hisanaga, K.Tanaka, and S.Murata (2007).
Rpn10-mediated degradation of ubiquitinated proteins is essential for mouse development.
  Mol Cell Biol, 27, 6629-6638.  
17098253 Y.Kang, N.Zhang, D.M.Koepp, and K.J.Walters (2007).
Ubiquitin receptor proteins hHR23a and hPLIC2 interact.
  J Mol Biol, 365, 1093-1101.  
16421449 E.D.Lowe, N.Hasan, J.F.Trempe, L.Fonso, M.E.Noble, J.A.Endicott, L.N.Johnson, and N.R.Brown (2006).
Structures of the Dsk2 UBL and UBA domains and their complex.
  Acta Crystallogr D Biol Crystallogr, 62, 177-188.
PDB codes: 2bwb 2bwe 2bwf
16497222 M.J.Hawryluk, P.A.Keyel, S.K.Mishra, S.C.Watkins, J.E.Heuser, and L.M.Traub (2006).
Epsin 1 is a polyubiquitin-selective clathrin-associated sorting protein.
  Traffic, 7, 262-281.  
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
16518384 S.L.Alam, and W.I.Sundquist (2006).
Two new structures of Ub-receptor complexes. U2.
  Nat Struct Mol Biol, 13, 186-188.  
17082762 T.Ishii, M.Funakoshi, and H.Kobayashi (2006).
Yeast Pth2 is a UBL domain-binding protein that participates in the ubiquitin-proteasome pathway.
  EMBO J, 25, 5492-5503.  
16122968 A.M.Bonvin, R.Boelens, and R.Kaptein (2005).
NMR analysis of protein interactions.
  Curr Opin Chem Biol, 9, 501-508.  
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
16138082 J.F.Trempe, N.R.Brown, E.D.Lowe, C.Gordon, I.D.Campbell, M.E.Noble, and J.A.Endicott (2005).
Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain.
  EMBO J, 24, 3178-3189.
PDB code: 1z96
16204249 J.Song, Z.Zhang, W.Hu, and Y.Chen (2005).
Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation.
  J Biol Chem, 280, 40122-40129.
PDB code: 2asq
15549676 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2003 commercial optical biosensor literature.
  J Mol Recognit, 18, 1.  
15949443 R.Varadan, M.Assfalg, S.Raasi, C.Pickart, and D.Fushman (2005).
Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain.
  Mol Cell, 18, 687-698.
PDB code: 1zo6
16056265 S.Elsasser, and D.Finley (2005).
Delivery of ubiquitinated substrates to protein-unfolding machines.
  Nat Cell Biol, 7, 742-749.  
16007098 S.Raasi, R.Varadan, D.Fushman, and C.M.Pickart (2005).
Diverse polyubiquitin interaction properties of ubiquitin-associated domains.
  Nat Struct Mol Biol, 12, 708-714.  
15987890 Y.G.Gao, A.X.Song, Y.H.Shi, Y.G.Chang, S.X.Liu, Y.Z.Yu, X.T.Cao, D.H.Lin, and H.Y.Hu (2005).
Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells.
  Protein Sci, 14, 2044-2050.
PDB code: 1ttn
15280365 B.E.Riley, Y.Xu, H.Y.Zoghbi, and H.T.Orr (2004).
The effects of the polyglutamine repeat protein ataxin-1 on the UbL-UBA protein A1Up.
  J Biol Chem, 279, 42290-42301.  
15473846 E.Morita, and W.I.Sundquist (2004).
Retrovirus budding.
  Annu Rev Cell Dev Biol, 20, 395-425.  
14585839 K.Fujiwara, T.Tenno, K.Sugasawa, J.G.Jee, I.Ohki, C.Kojima, H.Tochio, H.Hiroaki, F.Hanaoka, and M.Shirakawa (2004).
Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B.
  J Biol Chem, 279, 4760-4767.
PDB code: 1uel
15265035 M.Albrecht, M.Golatta, U.Wüllner, and T.Lengauer (2004).
Structural and functional analysis of ataxin-2 and ataxin-3.
  Eur J Biochem, 271, 3155-3170.  
15319427 M.J.May, S.E.Larsen, J.H.Shim, L.A.Madge, and S.Ghosh (2004).
A novel ubiquitin-like domain in IkappaB kinase beta is required for functional activity of the kinase.
  J Biol Chem, 279, 45528-45539.  
15322280 M.Kamionka, and J.Feigon (2004).
Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction.
  Protein Sci, 13, 2370-2377.
PDB code: 1tp4
15340068 M.L.Seibenhener, J.R.Babu, T.Geetha, H.C.Wong, N.R.Krishna, and M.W.Wooten (2004).
Sequestosome 1/p62 is a polyubiquitin chain binding protein involved in ubiquitin proteasome degradation.
  Mol Cell Biol, 24, 8055-8068.  
15086513 O.Tounekti, Y.Zhang, G.Klaiman, C.G.Goodyer, and A.LeBlanc (2004).
Proteasomal degradation of caspase-6 in 17beta-estradiol-treated neurons.
  J Neurochem, 89, 561-568.  
15209385 R.Hartmann-Petersen, and C.Gordon (2004).
Integral UBL domain proteins: a family of proteasome interacting proteins.
  Semin Cell Dev Biol, 15, 247-259.  
15117949 S.Elsasser, D.Chandler-Militello, B.Müller, J.Hanna, and D.Finley (2004).
Rad23 and Rpn10 serve as alternative ubiquitin receptors for the proteasome.
  J Biol Chem, 279, 26817-26822.  
15029239 S.L.Alam, J.Sun, M.Payne, B.D.Welch, B.K.Blake, D.R.Davis, H.H.Meyer, S.D.Emr, and W.I.Sundquist (2004).
Ubiquitin interactions of NZF zinc fingers.
  EMBO J, 23, 1411-1421.
PDB code: 1q5w
15155768 S.L.Miller, E.Malotky, and J.P.O'Bryan (2004).
Analysis of the role of ubiquitin-interacting motifs in ubiquitin binding and ubiquitylation.
  J Biol Chem, 279, 33528-33537.  
14707125 T.D.Mueller, M.Kamionka, and J.Feigon (2004).
Specificity of the interaction between ubiquitin-associated domains and ubiquitin.
  J Biol Chem, 279, 11926-11936.  
15053872 W.I.Sundquist, H.L.Schubert, B.N.Kelly, G.C.Hill, J.M.Holton, and C.P.Hill (2004).
Ubiquitin recognition by the human TSG101 protein.
  Mol Cell, 13, 783-789.
PDB code: 1s1q
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.