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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOPEPTIDASE, PEPTIDASE FAMILY M13A, B699Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 3.4.24
Find proteins for O53649 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore O53649 
Go to UniProtKB:  O53649
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / 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
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
CB [auth B], DB [auth B], EB [auth B], Z [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
211
Query on 211

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

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F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , KA [auth B] , L [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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ZN
Query on ZN

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

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AA [auth A] , BA [auth A] , CA [auth A] , DA [auth A] , EA [auth A] , FB [auth B] , GB [auth B] , HB [auth B] , 
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
 Ligand Interaction
CA
Query on CA

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

Download Ideal Coordinates CCD File 
HA [auth A], RB [auth B], TB [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDFKi :  35   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
D [auth A], JA [auth B]PHOSPHORAMIDONGlycopeptide /  Enzyme inhibitor

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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

View Full Validation Report



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