3L8G

Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli complexed with D-glycero-D-manno-heptose 1 ,7-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) .

Nguyen, H.H.Wang, L.Huang, H.Peisach, E.Dunaway-Mariano, D.Allen, K.N.

(2010) Biochemistry 49: 1082-1092

  • DOI: 10.1021/bi902019q
  • Primary Citation of Related Structures:  
    3L8E, 3L8F, 3L8G, 3L8H

  • PubMed Abstract: 
  • The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis ...

    The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D,D-heptose 1,7-bisphosphate phosphataseA187Escherichia coli K-12Mutation(s): 0 
Gene Names: b0200gmhBJW0196yaeD
EC: 3.1.3 (PDB Primary Data), 3.1.3.82 (UniProt)
UniProt
Find proteins for P63228 (Escherichia coli (strain K12))
Explore P63228 
Go to UniProtKB:  P63228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63228
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMB
Query on GMB

Download Ideal Coordinates CCD File 
E [auth A]1,7-di-O-phosphono-L-glycero-beta-D-manno-heptopyranose
C7 H16 O13 P2
LMTGTTLGDUACSJ-QQABCQGCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.669α = 90
b = 51.572β = 90
c = 52.185γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations