3ZUK

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (Zmp1), a Metalloprotease Involved in Pathogenicity.

Ferraris, D.M.Sbardella, D.Petrera, A.Marini, S.Amstutz, B.Coletta, M.Sander, P.Rizzi, M.

(2011) J Biol Chem 286: 32475

  • DOI: https://doi.org/10.1074/jbc.M111.271809
  • Primary Citation of Related Structures:  
    3ZUK

  • PubMed Abstract: 

    Mycobacterium tuberculosis, the causative agent of tuberculosis, parasitizes host macrophages. The resistance of the tubercle bacilli to the macrophage hostile environment relates to their ability to impair phagosome maturation and its fusion with the lysosome, thus preventing the formation of the phago-lysosome and eventually arresting the process of phagocytosis. The M. tuberculosis zinc-dependent metalloprotease Zmp1 has been proposed to play a key role in the process of phagosome maturation inhibition and emerged as an important player in pathogenesis. Here, we report the crystal structure of wild-type Zmp1 at 2.6 Å resolution in complex with the generic zinc metalloprotease inhibitor phosphoramidon, which we demonstrated to inhibit the enzyme potently. Our data represent the first structural characterization of a bacterial member of the zinc-dependent M13 endopeptidase family and revealed a significant degree of conservation with eukaryotic enzymes. However, structural comparison of the Zmp1-phosphoramidon complex with homologous human proteins neprilysin and endothelin-converting enzyme-1 revealed unique features of the Zmp1 active site to be exploited for the rational design of specific inhibitors that may prove useful as a pharmacological tool for better understanding Zmp1 biological function.


  • Organizational Affiliation

    DISCAFF Department of Chemical, Food, Pharmaceutical and Pharmacological Sciences, University of Piemonte Orientale A Avogadro, 28100 Novara, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDOPEPTIDASE, PEPTIDASE FAMILY M13
A, B
699Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 3.4.24
UniProt
Find proteins for O53649 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore O53649 
Go to UniProtKB:  O53649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53649
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RDF
Query on RDF

Download Ideal Coordinates CCD File 
D [auth A],
JA [auth B]
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
PG4
Query on PG4

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CB [auth B],
DB [auth B],
EB [auth B],
Z [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
U [auth A]
V [auth A]
W [auth A]
AB [auth B],
BB [auth B],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
ZA [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
211
Query on 211

Download Ideal Coordinates CCD File 
E [auth A]2,2',2''-NITRILOTRIETHANOL
C6 H15 N O3
GSEJCLTVZPLZKY-UHFFFAOYSA-N
PEG
Query on PEG

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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FA [auth A]
GA [auth A]
NB [auth B]
OB [auth B]
PB [auth B]
FA [auth A],
GA [auth A],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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C [auth A],
IA [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth B],
KB [auth B],
LB [auth B],
MB [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

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SB [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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HA [auth A],
RB [auth B],
TB [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
RDF PDBBind:  3ZUK Ki: 35 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.29α = 90
b = 198.77β = 90
c = 63.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
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: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-09-21
    Changes: Database references
  • Version 1.2: 2013-03-06
    Changes: Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description