5VO3

Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Literature

Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.

Nocek, B.Reidl, C.Starus, A.Heath, T.Bienvenue, D.Osipiuk, J.Jedrzejczak, R.Joachimiak, A.Becker, D.P.Holz, R.C.

(2018) Biochemistry 57: 574-584

  • DOI: 10.1021/acs.biochem.7b01151
  • Primary Citation of Related Structures:  
    5VO3

  • PubMed Abstract: 
  • The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10 ...

    The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclear Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn-Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ∼10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ∼10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. These data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.


    Organizational Affiliation

    Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-diaminopimelate desuccinylaseA380Haemophilus influenzaeMutation(s): 0 
Gene Names: dapEHI_0102
EC: 3.5.1.18
UniProt
Find proteins for P44514 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44514 
Go to UniProtKB:  P44514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44514
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
API
Query on API

Download Ideal Coordinates CCD File 
C [auth A]2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N
 Ligand Interaction
SIN
Query on SIN

Download Ideal Coordinates CCD File 
B [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.648α = 90
b = 135.536β = 90
c = 149.613γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2017-05-01 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Nocek, B.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release