PDBsum entry 1ip9

Go to PDB code: 
protein links
Signaling protein PDB id
Protein chain
85 a.a. *
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Solution structure of the pb1 domain of bem1p
Structure: Bem1 protein. Chain: a. Fragment: pb1 domain(residues 472-551). Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: H.Terasawa,Y.Noda,T.Ito,H.Hatanaka,S.Ichikawa,K.Ogura, H.Sumimoto,F.Inagaki
Key ref:
H.Terasawa et al. (2001). Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif. EMBO J, 20, 3947-3956. PubMed id: 11483498 DOI: 10.1093/emboj/20.15.3947
26-Apr-01     Release date:   15-Aug-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P29366  (BEM1_YEAST) -  Bud emergence protein 1
551 a.a.
85 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)


DOI no: 10.1093/emboj/20.15.3947 EMBO J 20:3947-3956 (2001)
PubMed id: 11483498  
Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif.
H.Terasawa, Y.Noda, T.Ito, H.Hatanaka, S.Ichikawa, K.Ogura, H.Sumimoto, F.Inagaki.
PB1 domains are novel protein modules capable of binding to target proteins that contain PC motifs. We report here the NMR structure and ligand-binding site of the PB1 domain of the cell polarity establishment protein, Bem1p. In addition, we identify the topology of the PC motif-containing region of Cdc24p by NMR, another cell polarity establishment protein that interacts with Bem1p. The PC motif-containing region is a structural domain offering a scaffold to the PC motif. The chemical shift perturbation experiment and the mutagenesis study show that the PC motif is a major structural element that binds to the PB1 domain. A structural database search reveals close similarity between the Bem1p PB1 domain and the c-Raf1 Ras-binding domain. However, these domains are functionally distinct from each other.
  Selected figure(s)  
Figure 1.
Figure 1 2D 1H-15N HSQC spectra of (A) Bem PB1 and (B) Cdc24p PCCR. The cross peaks are labeled with one-letter codes of amino acids and residue numbers (SC denotes side-chain resonances). Position 6 of Bem PB1 and Cdc24p PCCR corresponds to residue 472 of Bem1p and 780 of Cdc24p, respectively.
Figure 2.
Figure 2 The 3D structure of Bem PB1. The overall fold of amino acid residues 12 -85 of Bem PB1 is depicted, with the N- and C-termini labeled. (A) Overlay of the 20 final conformers on the average coordinate position for the backbone (N, C^ and C') atoms of residues 12 -55 and 62 -85. Residue numbers corresponding to the beginning and the end of each secondary structural element are shown. (B) Ribbon diagrams of the minimized mean structure of Bem PB1. Both figures were created using the program MOLSCRIPT (Kraulis, 1991). Two of the inner strands ( 1 and 4) are parallel and can be seen in orange, with the other two strands ( 2 and 3) running in an antiparallel manner shown in yellow. The first -helix is shown in dark green and the second one is shown in light green. The notations of these secondary structural elements (a, -helix; b, -strand) are indicated.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 3947-3956) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21415856 M.P.Luna-Vargas, A.C.Faesen, W.J.van Dijk, M.Rape, A.Fish, and T.K.Sixma (2011).
Ubiquitin-specific protease 4 is inhibited by its ubiquitin-like domain.
  EMBO Rep, 12, 365-372.
PDB code: 2y6e
20930476 F.Inagaki (2010).
[On the occasion of retirement from Graduate School of Pharmaceutical Sciences, Hokkaido University].
  Yakugaku Zasshi, 130, 1251-1262.  
19451149 K.Ogura, T.Tandai, S.Yoshinaga, Y.Kobashigawa, H.Kumeta, T.Ito, H.Sumimoto, and F.Inagaki (2009).
NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae.
  J Biochem, 146, 317-325.
PDB codes: 2kfj 2kfk
19909509 M.T.Ehebauer, and A.M.Arias (2009).
The structural and functional determinants of the Axin and Dishevelled DIX domains.
  BMC Struct Biol, 9, 70.  
19208825 W.Guo, S.Wu, L.Wang, R.Y.Wang, X.Wei, J.Liu, and B.Fang (2009).
Interruption of RNA processing machinery by a small compound, 1-[(4-chlorophenyl)methyl]-1H-indole-3-carboxaldehyde (oncrasin-1).
  Mol Cancer Ther, 8, 441-448.  
18513324 H.Sumimoto (2008).
Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species.
  FEBS J, 275, 3249-3277.  
17347519 H.O.Park, and E.Bi (2007).
Central roles of small GTPases in the development of cell polarity in yeast and beyond.
  Microbiol Mol Biol Rev, 71, 48-96.  
17290225 K.Honbou, R.Minakami, S.Yuzawa, R.Takeya, N.N.Suzuki, S.Kamakura, H.Sumimoto, and F.Inagaki (2007).
Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding.
  EMBO J, 26, 1176-1186.
PDB code: 2dyb
17476308 W.Feng, H.Wu, L.N.Chan, and M.Zhang (2007).
The Par-3 NTD adopts a PB1-like structure required for Par-3 oligomerization and membrane localization.
  EMBO J, 26, 2786-2796.
PDB code: 2ns5
17140284 A.B.Goryachev, and A.V.Pokhilko (2006).
Computational model explains high activity and rapid cycling of Rho GTPases within protein complexes.
  PLoS Comput Biol, 2, e172.  
16949360 J.Moscat, M.T.Diaz-Meco, A.Albert, and S.Campuzano (2006).
Cell signaling and function organized by PB1 domain interactions.
  Mol Cell, 23, 631-640.  
16322752 J.Moscat, P.Rennert, and M.T.Diaz-Meco (2006).
PKCzeta at the crossroad of NF-kappaB and Jak1/Stat6 signaling pathways.
  Cell Death Differ, 13, 702-711.  
16507987 K.Nakamura, M.T.Uhlik, N.L.Johnson, K.M.Hahn, and G.L.Johnson (2006).
PB1 domain-dependent signaling complex is required for extracellular signal-regulated kinase 5 activation.
  Mol Cell Biol, 26, 2065-2079.  
15712318 M.Jenny, O.A.Wrulich, W.Schwaiger, and F.Ueberall (2005).
Relevance of atypical protein kinase C isotypes to the drug discovery process.
  Chembiochem, 6, 491-499.  
15772751 M.Schubert, D.Labudde, D.Leitner, H.Oschkinat, and P.Schmieder (2005).
A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments.
  J Biomol NMR, 31, 115-128.  
15590654 Y.Hirano, S.Yoshinaga, R.Takeya, N.N.Suzuki, M.Horiuchi, M.Kohjima, H.Sumimoto, and F.Inagaki (2005).
Structure of a cell polarity regulator, a complex between atypical PKC and Par6 PB1 domains.
  J Biol Chem, 280, 9653-9661.
PDB code: 1wmh
15364906 B.L.Lytle, F.C.Peterson, S.H.Qiu, M.Luo, Q.Zhao, J.L.Markley, and B.F.Volkman (2004).
Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B.
  J Biol Chem, 279, 46787-46793.
PDB code: 1t0y
15265004 K.Sugawara, N.N.Suzuki, Y.Fujioka, N.Mizushima, Y.Ohsumi, and F.Inagaki (2004).
The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8.
  Genes Cells, 9, 611-618.
PDB code: 1ugm
15143057 Y.Hirano, S.Yoshinaga, K.Ogura, M.Yokochi, Y.Noda, H.Sumimoto, and F.Inagaki (2004).
Solution structure of atypical protein kinase C PB1 domain and its mode of interaction with ZIP/p62 and MEK5.
  J Biol Chem, 279, 31883-31890.
PDB code: 1vd2
12912994 K.Nakamura, and G.L.Johnson (2003).
PB1 domains of MEKK2 and MEKK3 interact with the MEK5 PB1 domain for activation of the ERK5 pathway.
  J Biol Chem, 278, 36989-36992.  
12409291 M.Endo, M.Shirouzu, and S.Yokoyama (2003).
The Cdc42 binding and scaffolding activities of the fission yeast adaptor protein Scd2.
  J Biol Chem, 278, 843-852.  
12692530 M.H.Kim, T.Cierpicki, U.Derewenda, D.Krowarsch, Y.Feng, Y.Devedjiev, Z.Dauter, C.A.Walsh, J.Otlewski, J.H.Bushweller, and Z.S.Derewenda (2003).
The DCX-domain tandems of doublecortin and doublecortin-like kinase.
  Nat Struct Biol, 10, 324-333.
PDB codes: 1mfw 1mg4 1mjd
12887891 M.I.Wilson, D.J.Gill, O.Perisic, M.T.Quinn, and R.L.Williams (2003).
PB1 domain-mediated heterodimerization in NADPH oxidase and signaling complexes of atypical protein kinase C with Par6 and p62.
  Mol Cell, 12, 39-50.
PDB code: 1oey
14517229 S.Yoshinaga, M.Kohjima, K.Ogura, M.Yokochi, R.Takeya, T.Ito, H.Sumimoto, and F.Inagaki (2003).
The PB1 domain and the PC motif-containing region are structurally similar protein binding modules.
  EMBO J, 22, 4888-4897.
PDB code: 1q1o
12813044 T.Lamark, M.Perander, H.Outzen, K.Kristiansen, A.Øvervatn, E.Michaelsen, G.Bjørkøy, and T.Johansen (2003).
Interaction codes within the family of mammalian Phox and Bem1p domain-containing proteins.
  J Biol Chem, 278, 34568-34581.  
12920115 Y.Noda, M.Kohjima, T.Izaki, K.Ota, S.Yoshinaga, F.Inagaki, T.Ito, and H.Sumimoto (2003).
Molecular recognition in dimerization between PB1 domains.
  J Biol Chem, 278, 43516-43524.  
11927541 A.C.Butty, N.Perrinjaquet, A.Petit, M.Jaquenoud, J.E.Segall, K.Hofmann, C.Zwahlen, and M.Peter (2002).
A positive feedback loop stabilizes the guanine-nucleotide exchange factor Cdc24 at sites of polarization.
  EMBO J, 21, 1565-1576.  
11796218 C.P.Ponting, T.Ito, J.Moscat, M.T.Diaz-Meco, F.Inagaki, and H.Sumimoto (2002).
OPR, PC and AID: all in the PB1 family.
  Trends Biochem Sci, 27, 10.  
12456638 F.Kuribayashi, H.Nunoi, K.Wakamatsu, S.Tsunawaki, K.Sato, T.Ito, and H.Sumimoto (2002).
The adaptor protein p40(phox) as a positive regulator of the superoxide-producing phagocyte oxidase.
  EMBO J, 21, 6312-6320.  
11796224 J.H.Hurley, D.E.Anderson, B.Beach, B.Canagarajah, Y.S.Ho, E.Jones, G.Miller, S.Misra, M.Pearson, L.Saidi, S.Suer, R.Trievel, and Y.Tsujishita (2002).
Structural genomics and signaling domains.
  Trends Biochem Sci, 27, 48-53.  
11483497 T.Ito, Y.Matsui, T.Ago, K.Ota, and H.Sumimoto (2001).
Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions.
  EMBO J, 20, 3938-3946.  
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.