3ETN

Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications.

Chiu, H.J.Grant, J.C.Farr, C.L.Jaroszewski, L.Knuth, M.W.Miller, M.D.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2640-2651

  • DOI: 10.1107/S1399004714017052
  • Primary Citation of Related Structures:  
    3ETN

  • PubMed Abstract: 
  • The crystal structure of arabinose-5-phosphate isomerase (API) from Bacteroides fragilis (bfAPI) was determined at 1.7 Å resolution and was found to be a tetramer of a single-domain sugar isomerase (SIS) with an endogenous ligand, CMP-Kdo (cytidine 5'-monophosphate-3-deoxy-D-manno-oct-2-ulosonate), bound at the active site ...

    The crystal structure of arabinose-5-phosphate isomerase (API) from Bacteroides fragilis (bfAPI) was determined at 1.7 Å resolution and was found to be a tetramer of a single-domain sugar isomerase (SIS) with an endogenous ligand, CMP-Kdo (cytidine 5'-monophosphate-3-deoxy-D-manno-oct-2-ulosonate), bound at the active site. API catalyzes the reversible isomerization of D-ribulose 5-phosphate to D-arabinose 5-phosphate in the first step of the Kdo biosynthetic pathway. Interestingly, the bound CMP-Kdo is neither the substrate nor the product of the reaction catalyzed by API, but corresponds to the end product in the Kdo biosynthetic pathway and presumably acts as a feedback inhibitor for bfAPI. The active site of each monomer is located in a surface cleft at the tetramer interface between three monomers and consists of His79 and His186 from two different adjacent monomers and a Ser/Thr-rich region, all of which are highly conserved across APIs. Structure and sequence analyses indicate that His79 and His186 may play important catalytic roles in the isomerization reaction. CMP-Kdo mimetics could therefore serve as potent and specific inhibitors of API and provide broad protection against many different bacterial infections.


    Organizational Affiliation

    Joint Center for Structural Genomics, http://www.jcsg.org, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative phosphosugar isomerase involved in capsule formationA, B, C, D220Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: YP_209877.1BF0137BF9343_0136
Find proteins for Q5LIW1 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / JCM 11019 / NCTC 9343))
Explore Q5LIW1 
Go to UniProtKB:  Q5LIW1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMK
Query on CMK

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], M [auth C], O [auth D]CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
C17 H26 N3 O15 P
YWWJKULNWGRYAS-UOVSKDHASA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , J [auth B] , K [auth B] , L [auth B] , N [auth C] , P [auth D] , 
F [auth A],  G [auth A],  H [auth A],  J [auth B],  K [auth B],  L [auth B],  N [auth C],  P [auth D],  Q [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.409α = 90
b = 114.267β = 90
c = 115.917γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-11-05
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description