4XZZ

Structure of Helicobacter pylori Csd6 in the ligand-free state

  • Classification: HYDROLASE
  • Organism(s): Helicobacter pylori 26695
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2015-02-05 Released: 2015-09-02 
  • Deposition Author(s): Kim, H.S., Im, H.N., Yoon, H.J., Suh, S.W.
  • Funding Organization(s): National Research Foundation, Korea Ministry of Health, Welfare & Family Affairs, Korea Ministry of Education, The Ministry of Science, ICT and Future Planning, and the National Research Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of l,d-Carboxypeptidase

Kim, H.S.Im, H.N.An, D.R.Yoon, J.Y.Jang, J.Y.Mobashery, S.Hesek, D.Lee, M.Yoo, J.Cui, M.Choi, S.Kim, C.Lee, N.K.Kim, S.J.Kim, J.Y.Bang, G.Han, B.W.Lee, B.I.Yoon, H.J.Suh, S.W.

(2015) J Biol Chem 290: 25103-25117

  • DOI: 10.1074/jbc.M115.658781
  • Primary Citation of Related Structures:  
    4XZZ, 4Y4V

  • PubMed Abstract: 
  • Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides ...

    Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of l,d-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known l,d-transpeptidases. Mass analyses confirm that Csd6 functions only as an l,d-carboxypeptidase and not as an l,d-transpeptidase. The d-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of l,d-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.


    Organizational Affiliation

    From the Departments of Chemistry and Biophysics and Chemical Biology, College of Natural Sciences, and sewonsuh@snu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved hypothetical secreted proteinA, B339Helicobacter pylori 26695Mutation(s): 0 
Gene Names: C694_02665HP_0518
UniProt
Find proteins for O25255 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25255 
Go to UniProtKB:  O25255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25255
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.963α = 90
b = 91.028β = 90
c = 127.799γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research FoundationKorea, Republic Of2013R1A2A1A05067303
Korea Ministry of Health, Welfare & Family AffairsKorea, Republic OfA092006
Korea Ministry of EducationKorea, Republic Of2012-039930
Korea Ministry of EducationKorea, Republic Of2014R1A1A3A04050250
The Ministry of Science, ICT and Future Planning, and the National Research FoundationKorea, Republic Of2011-0028885
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI090348

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 1.3: 2017-10-18
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.4: 2022-03-23
    Changes: Author supporting evidence, Database references