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PDBsum entry 1jhj

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protein metals links
Cell cycle PDB id
1jhj
Jmol
Contents
Protein chain
161 a.a. *
Metals
_NI
Waters ×157
* Residue conservation analysis
PDB id:
1jhj
Name: Cell cycle
Title: Crystal structure of the apc10/doc1 subunit of the human anaphase-promoting complex
Structure: Apc10. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.209     R-free:   0.244
Authors: K.S.Wendt,H.C.Vodermaier,U.Jacob,C.Gieffers,M.Gmachl,J.- M.Peters,R.Huber,P.Sondermann
Key ref:
K.S.Wendt et al. (2001). Crystal structure of the APC10/DOC1 subunit of the human anaphase-promoting complex. Nat Struct Biol, 8, 784-788. PubMed id: 11524682 DOI: 10.1038/nsb0901-784
Date:
28-Jun-01     Release date:   24-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UM13  (APC10_HUMAN) -  Anaphase-promoting complex subunit 10
Seq:
Struc:
185 a.a.
161 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     protein K11-linked ubiquitination   15 terms 
  Biochemical function     ubiquitin-protein ligase activity     1 term  

 

 
DOI no: 10.1038/nsb0901-784 Nat Struct Biol 8:784-788 (2001)
PubMed id: 11524682  
 
 
Crystal structure of the APC10/DOC1 subunit of the human anaphase-promoting complex.
K.S.Wendt, H.C.Vodermaier, U.Jacob, C.Gieffers, M.Gmachl, J.M.Peters, R.Huber, P.Sondermann.
 
  ABSTRACT  
 
The anaphase-promoting complex (APC), or cyclosome, is a cell cycle-regulated ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC is composed of at least 11 subunits; no structure has been determined for any of these subunits. The subunit APC10/DOC1, a one-domain protein consisting of 185 amino acids, has a conserved core (residues 22-161) that is homologous to domains found in several other putative ubiquitin ligases and, therefore, may play a role in ubiquitination reactions. Here we report the crystal structure of human APC10 at 1.6 A resolution. The core of the protein is formed by a beta-sandwich that adopts a jellyroll fold. Unexpectedly, this structure is highly similar to ligand-binding domains of several bacterial and eukaryotic proteins, such as galactose oxidase and coagulation factor Va, raising the possibility that APC10 may function by binding a yet unidentified ligand. We further provide biochemical evidence that the C-terminus of APC10 binds to CDC27/APC3, an APC subunit that contains multiple tetratrico peptide repeats.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of human APC10. a, Stereo view with labeled secondary structure elements. The sheets forming both sides of the -sandwich are colored green and orange; -helices, violet; the small -sheet, gray; and the separate 0 strand, blue. The side chains of residues Ser 35, Trp 54 and Asp 57 are drawn as ball-and-sticks. b, Stereo view of the superimposed worm diagrams of human APC10 (red), D1 domain of galactose oxidase (green; PDB entry 1GOH) and the galactose binding domain of sialidase of the ribbon diagram (blue; PDB entry 1EUU). The galactose molecule bound to both the galatose oxidase and the sialidase is shown. Both figures were generated with MOLSCRIPT29 and Raster3D^30. c, Final model and stereo view of the final 2F[o] - F[c] map around Ser 35 contoured at 1 . The hydrogen bonds between Ser 35, Trp 54 and Asp 57 are drawn in magenta. The figure was generated with BOBSCRIPT31 and RASTER3D^30.
Figure 2.
Figure 2. The electrostatic surface potential, from negative (red) to positive (blue), is mapped on a solid surface representation of APC10. a, N-terminal loop region with the potential ligand binding site. b, Orientation the same as in Fig. 1a. c, C-terminal loop region with a high concentration of positive charges. Figure was generated with GRASP32.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 784-788) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21307936 A.Schreiber, F.Stengel, Z.Zhang, R.I.Enchev, E.H.Kong, E.P.Morris, C.V.Robinson, P.C.da Fonseca, and D.Barford (2011).
Structural basis for the subunit assembly of the anaphase-promoting complex.
  Nature, 470, 227-232.  
21186364 B.A.Buschhorn, G.Petzold, M.Galova, P.Dube, C.Kraft, F.Herzog, H.Stark, and J.M.Peters (2011).
Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1.
  Nat Struct Mol Biol, 18, 6.  
21092369 D.Barford (2011).
Structure, function and mechanism of the anaphase promoting complex (APC/C).
  Q Rev Biophys, 44, 153-190.  
21307929 I.Foe, and D.Toczyski (2011).
Structural biology: a new look for the APC.
  Nature, 470, 182-183.  
  21261459 J.R.McLean, D.Chaix, M.D.Ohi, and K.L.Gould (2011).
State of the APC/C: organization, function, and structure.
  Crit Rev Biochem Mol Biol, 46, 118-136.  
21107322 P.C.da Fonseca, E.H.Kong, Z.Zhang, A.Schreiber, M.A.Williams, E.P.Morris, and D.Barford (2011).
Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
  Nature, 470, 274-278.  
20939100 S.Kalkhof, S.Haehn, M.Paulsson, N.Smyth, J.Meiler, and A.Sinz (2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
  Proteins, 78, 3409-3427.  
20232159 W.B.He, Z.W.Wang, Y.Li, Z.L.Tang, S.L.Yang, Y.L.Mu, K.M.Peng, and K.Li (2010).
Sequence characterization and promoter identification of porcine APC10 gene.
  Mol Biol Rep, 37, 3841-3849.  
20924356 Z.Zhang, K.Kulkarni, S.J.Hanrahan, A.J.Thompson, and D.Barford (2010).
The APC/C subunit Cdc16/Cut9 is a contiguous tetratricopeptide repeat superhelix with a homo-dimer interface similar to Cdc27.
  EMBO J, 29, 3733-3744.
PDB code: 2xpi
19657357 D.C.Crawford, N.Zheng, E.C.Speelmon, I.Stanaway, M.J.Rieder, D.A.Nickerson, M.J.McElrath, and J.Lingappa (2009).
An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1.
  Genes Immun, 10, 715-721.  
18816799 T.A.Ramelot, S.Raman, A.P.Kuzin, R.Xiao, L.C.Ma, T.B.Acton, J.F.Hunt, G.T.Montelione, D.Baker, and M.A.Kennedy (2009).
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
  Proteins, 75, 147-167.
PDB codes: 1tvg 1xpw
17977833 C.M.Van Itallie, L.Betts, J.G.Smedley, B.A.McClane, and J.M.Anderson (2008).
Structure of the claudin-binding domain of Clostridium perfringens enterotoxin.
  J Biol Chem, 283, 268-274.
PDB code: 2quo
19026776 J.A.Benanti, and D.P.Toczyski (2008).
Cdc20, an activator at last.
  Mol Cell, 32, 460-461.  
18384150 K.S.Aragão, M.Satre, A.Imberty, and A.Varrot (2008).
Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.
  Proteins, 73, 43-52.
PDB codes: 2vm9 2vmc 2vmd 2vme
18544349 R.van Leuken, L.Clijsters, and R.Wolthuis (2008).
To cell cycle, swing the APC/C.
  Biochim Biophys Acta, 1786, 49-59.  
19026787 Y.Kimata, J.E.Baxter, A.M.Fry, and H.Yamano (2008).
A role for the Fizzy/Cdc20 family of proteins in activation of the APC/C distinct from substrate recruitment.
  Mol Cell, 32, 576-583.  
18082611 M.D.Ohi, A.Feoktistova, L.Ren, C.Yip, Y.Cheng, J.S.Chen, H.J.Yoon, J.S.Wall, Z.Huang, P.A.Penczek, K.L.Gould, and T.Walz (2007).
Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1.
  Mol Cell, 28, 871-885.  
17031559 R.M.Beaty, J.B.Edwards, K.Boon, I.M.Siu, J.E.Conway, and G.J.Riggins (2007).
PLXDC1 (TEM7) is identified in a genome-wide expression screen of glioblastoma endothelium.
  J Neurooncol, 81, 241-248.  
16481473 B.R.Thornton, T.M.Ng, M.E.Matyskiela, C.W.Carroll, D.O.Morgan, and D.P.Toczyski (2006).
An architectural map of the anaphase-promoting complex.
  Genes Dev, 20, 449-460.  
16251191 E.W.Odom, and G.R.Vasta (2006).
Characterization of a binary tandem domain F-type lectin from striped bass (Morone saxatilis).
  J Biol Chem, 281, 1698-1713.  
16950791 H.J.Yoon, A.Feoktistova, J.S.Chen, J.L.Jennings, A.J.Link, and K.L.Gould (2006).
Role of Hcn1 and its phosphorylation in fission yeast anaphase-promoting complex/cyclosome function.
  J Biol Chem, 281, 32284-32293.  
16896351 J.M.Peters (2006).
The anaphase promoting complex/cyclosome: a machine designed to destroy.
  Nat Rev Mol Cell Biol, 7, 644-656.  
16648845 M.J.Hayes, Y.Kimata, S.L.Wattam, C.Lindon, G.Mao, H.Yamano, and A.M.Fry (2006).
Early mitotic degradation of Nek2A depends on Cdc20-independent interaction with the APC/C.
  Nat Cell Biol, 8, 607-614.  
15911580 A.M.Page, V.Aneliunas, J.R.Lamb, and P.Hieter (2005).
In vivo characterization of the nonessential budding yeast anaphase-promoting complex/cyclosome components Swm1p, Mnd2p and Apc9p.
  Genetics, 170, 1045-1062.  
15649358 C.W.Carroll, M.Enquist-Newman, and D.O.Morgan (2005).
The APC subunit Doc1 promotes recognition of the substrate destruction box.
  Curr Biol, 15, 11-18.  
16364911 L.A.Passmore, C.R.Booth, C.Vénien-Bryan, S.J.Ludtke, C.Fioretto, L.N.Johnson, W.Chiu, and D.Barford (2005).
Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation.
  Mol Cell, 20, 855-866.  
16364912 P.Dube, F.Herzog, C.Gieffers, B.Sander, D.Riedel, S.A.Müller, A.Engel, J.M.Peters, and H.Stark (2005).
Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C.
  Mol Cell, 20, 867-879.  
15144564 C.Nourry, L.Maksumova, M.Pang, X.Liu, and T.Wang (2004).
Direct interaction between Smad3, APC10, CDH1 and HEF1 in proteasomal degradation of HEF1.
  BMC Cell Biol, 5, 20.  
15465324 G.R.Vasta, H.Ahmed, and E.W.Odom (2004).
Structural and functional diversity of lectin repertoires in invertebrates, protochordates and ectothermic vertebrates.
  Curr Opin Struct Biol, 14, 617-630.  
12956947 H.C.Vodermaier, C.Gieffers, S.Maurer-Stroh, F.Eisenhaber, and J.M.Peters (2003).
TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1.
  Curr Biol, 13, 1459-1468.  
12429094 A.Stocker, T.Tomizaki, C.Schulze-Briese, and U.Baumann (2002).
Crystal structure of the human supernatant protein factor.
  Structure, 10, 1533-1540.
PDB code: 1o6u
12402045 C.W.Carroll, and D.O.Morgan (2002).
The Doc1 subunit is a processivity factor for the anaphase-promoting complex.
  Nat Cell Biol, 4, 880-887.  
12481031 D.C.Dias, G.Dolios, R.Wang, and Z.Q.Pan (2002).
CUL7: A DOC domain-containing cullin selectively binds Skp1.Fbx29 to form an SCF-like complex.
  Proc Natl Acad Sci U S A, 99, 16601-16606.  
12049731 J.M.Peters (2002).
The anaphase-promoting complex: proteolysis in mitosis and beyond.
  Mol Cell, 9, 931-943.  
12091873 M.A.Bianchet, E.W.Odom, G.R.Vasta, and L.M.Amzel (2002).
A novel fucose recognition fold involved in innate immunity.
  Nat Struct Biol, 9, 628-634.
PDB code: 1k12
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.