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PDBsum entry 1zxj

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protein Protein-protein interface(s) links
Structural genomics, unknown function PDB id
1zxj
Jmol
Contents
Protein chains
192 a.a. *
171 a.a. *
193 a.a. *
Waters ×14
* Residue conservation analysis
PDB id:
1zxj
Name: Structural genomics, unknown function
Title: Crystal structure of the hypthetical mycoplasma protein, mpn555
Structure: Hypothetical protein mg377 homolog. Chain: a, b, c, d. Synonym: mpn555. Engineered: yes
Source: Mycoplasma pneumoniae. Organism_taxid: 2104. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.248     R-free:   0.322
Authors: U.Schulze-Gahmen,S.Aono,C.Shengfeng,H.Yokota,R.Kim,S.-H.Kim, Berkeley Structural Genomics Center (Bsgc)
Key ref:
U.Schulze-Gahmen et al. (2005). Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function. Acta Crystallogr D Biol Crystallogr, 61, 1343-1347. PubMed id: 16204885 DOI: 10.1107/S090744490502264X
Date:
08-Jun-05     Release date:   26-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P75223  (Y555_MYCPN) -  Uncharacterized protein MG377 homolog
Seq:
Struc:
193 a.a.
192 a.a.*
Protein chain
Pfam   ArchSchema ?
P75223  (Y555_MYCPN) -  Uncharacterized protein MG377 homolog
Seq:
Struc:
193 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P75223  (Y555_MYCPN) -  Uncharacterized protein MG377 homolog
Seq:
Struc:
193 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein transport   2 terms 

 

 
DOI no: 10.1107/S090744490502264X Acta Crystallogr D Biol Crystallogr 61:1343-1347 (2005)
PubMed id: 16204885  
 
 
Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function.
U.Schulze-Gahmen, S.Aono, S.Chen, H.Yokota, R.Kim, S.H.Kim.
 
  ABSTRACT  
 
The crystal structure of the hypothetical protein MPN555 from Mycoplasma pneumoniae (gi|1673958) has been determined to a resolution of 2.8 Angstrom using anomalous diffraction data at the Se-peak wavelength. Structure determination revealed a mostly alpha-helical protein with a three-lobed shape. The three lobes or fingers delineate a central binding groove and additional grooves between lobes 1 and 3 and between lobes 2 and 3. For one of the molecules in the asymmetric unit, the central binding pocket was filled with a peptide from the uncleaved N-terminal affinity tag. The MPN555 structure has structural homology to two bacterial chaperone proteins: SurA and trigger factor from Escherichia coli. The structural data and the homology to other chaperone proteins suggests an involvement in protein folding as a molecular chaperone for MPN555.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Overall fold and surface representation of MPN555. Molecule D was chosen for the schematic drawings in this figure and Fig. 4[98] [link]-[99][turqarr.gif] because it has the most complete N-terminal peptide originating from the affinity tag. (a) shows the arrangement of secondary structures into three lobes in the MPN555 fold. A peptide from the N-terminal His tag is bound in the central binding pocket. (b) shows a surface representation of the same molecules. Negatively charged surfaces are colored in red and positively charged surfaces in blue. Electrostatic surfaces were calculated using the program APBS (Baker et al., 2001[100] [Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.]-[101][bluearr.gif] ) in PyMOL.
Figure 4.
Figure 4 Superposition of two structurally homologous proteins onto MPN555. (a) Parts of the N-terminal and C-terminal segments of SurA (PDB code [116]1m5y ) were superimposed onto MPN555 with the program PDBSET from the CCP4 suite using matrices suggested by the DALI search engine. The r.m.s.d. for 139 aligned residues is 4.7 . MPN555 is shown in red. The complete SurA protein is shown in blue. (b) A similar superposition of the C-terminal domain of E. coli trigger factor (PDB code [117]1w26 ) onto MPN555. The r.m.s.d. for 129 aligned residues is 3.5 . MPN555 is shown in red and the C-terminal domain of TF is shown in green.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1343-1347) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17348019 D.Das, H.Hyun, Y.Lou, H.Yokota, R.Kim, and S.H.Kim (2007).
Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae.
  Proteins, 67, 776-782.
PDB code: 2hql
17764033 D.H.Shin, J.Hou, J.M.Chandonia, D.Das, I.G.Choi, R.Kim, and S.H.Kim (2007).
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.
  J Struct Funct Genomics, 8, 99.  
17296610 S.K.Lakshmipathy, S.Tomic, C.M.Kaiser, H.C.Chang, P.Genevaux, C.Georgopoulos, J.M.Barral, A.E.Johnson, F.U.Hartl, and S.A.Etchells (2007).
Identification of nascent chain interaction sites on trigger factor.
  J Biol Chem, 282, 12186-12193.  
16926148 F.Merz, A.Hoffmann, A.Rutkowska, B.Zachmann-Brand, B.Bukau, and E.Deuerling (2006).
The C-terminal domain of Escherichia coli trigger factor represents the central module of its chaperone activity.
  J Biol Chem, 281, 31963-31971.  
17021621 P.C.Stirling, S.F.Bakhoum, A.B.Feigl, and M.R.Leroux (2006).
Convergent evolution of clamp-like binding sites in diverse chaperones.
  Nat Struct Mol Biol, 13, 865-870.  
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