Crystal structure of HmrA

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural and Functional Analyses Reveal That Staphylococcus aureus Antibiotic Resistance Factor HmrA Is a Zinc-dependent Endopeptidase.

Botelho, T.O.Guevara, T.Marrero, A.Arede, P.Fluxa, V.S.Reymond, J.L.Oliveira, D.C.Gomis-Ruth, F.X.

(2011) J Biol Chem 286: 25697-25709

  • DOI: https://doi.org/10.1074/jbc.M111.247437
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    HmrA is an antibiotic resistance factor of methicillin-resistant Staphylococcus aureus. Molecular analysis of this protein revealed that it is not a muramidase or β-lactamase but a nonspecific double-zinc endopeptidase consisting of a catalytic domain and an inserted oligomerization domain, which probably undergo a relative interdomain hinge rotation upon substrate binding. The active-site cleft is located at the domain interface. Four HmrA protomers assemble to a large ∼170-kDa homotetrameric complex of 125 Å. All four active sites are fully accessible and ∼50-70 Å apart, far enough apart to act on a large meshwork substrate independently but simultaneously. In vivo studies with four S. aureus strains of variable resistance levels revealed that the extracellular addition of HmrA protects against loss of viability in the presence of oxacillin and that this protection depends on proteolytic activity. All of these results indicate that HmrA is a peptidase that participates in resistance mechanisms in vivo in the presence of β-lactams. Furthermore, our results have implications for most S. aureus strains of known genomic sequences and several other cocci and bacilli, which harbor close orthologs. This suggests that HmrA may be a new widespread antibiotic resistance factor in bacteria.

  • Organizational Affiliation

    Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Barcelona Science Park, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HmrA protein
A, B, C, D
394Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: hmrASA1935
Find proteins for A0A0H3JVA7 (Staphylococcus aureus (strain N315))
Explore A0A0H3JVA7 
Go to UniProtKB:  A0A0H3JVA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JVA7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
EA [auth C]
FA [auth C]
G [auth A]
GA [auth C]
AA [auth B],
EA [auth C],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
PA [auth D],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth C]
DA [auth C]
E [auth A]
F [auth A]
BA [auth B],
CA [auth C],
DA [auth C],
E [auth A],
F [auth A],
LA [auth D],
MA [auth D],
P [auth B],
Q [auth B]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.73α = 90
b = 132.73β = 90
c = 336.89γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references