3RAM | pdb_00003ram

Crystal structure of HmrA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.218 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

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 Biological Chem 286: 25697-25709

  • DOI: https://doi.org/10.1074/jbc.M111.247437
  • Primary Citation Related Structures: 
    3RAM

  • 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.

Macromolecule Content 

  • Total Structure Weight: 176.36 kDa 
  • Atom Count: 12,547 
  • Modeled Residue Count: 1,561 
  • Deposited Residue Count: 1,576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HmrA protein
A, B, C, D
394Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: hmrASA1935

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.218 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
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
SHELXSphasing
REFMACrefinement
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
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary