PDBsum entry 3hsa

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protein ligands Protein-protein interface(s) links
Structural genomics, unknown function PDB id
Protein chains
125 a.a. *
112 a.a. *
GOL ×6
PEG ×2
Waters ×242
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Crystal structure of pleckstrin homology domain (yp_926556.1 shewanella amazonensis sb2b at 1.99 a resolution
Structure: Pleckstrin homology domain. Chain: a, b, c, d, e. Engineered: yes
Source: Shewanella amazonensis sb2b. Organism_taxid: 326297. Gene: sama_0678, yp_926556.1. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.99Å     R-factor:   0.191     R-free:   0.233
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref: Q.Xu et al. (2010). Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J Mol Biol, 396, 31-46. PubMed id: 19913036
10-Jun-09     Release date:   23-Jun-09    
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Protein chains
Pfam   ArchSchema ?
A1S3D0  (A1S3D0_SHEAM) -  Uncharacterized protein
125 a.a.
125 a.a.*
Protein chains
Pfam   ArchSchema ?
A1S3D0  (A1S3D0_SHEAM) -  Uncharacterized protein
125 a.a.
112 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 22 residue positions (black crosses)


J Mol Biol 396:31-46 (2010)
PubMed id: 19913036  
Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.
Q.Xu, A.Bateman, R.D.Finn, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, D.Ernst, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C(5) symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C(12) symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.