3DL1

Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.20 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Structure of Mlc Titration Factor A (MtfA/YeeI) Reveals a Prototypical Zinc Metallopeptidase Related to Anthrax Lethal Factor.

Xu, Q.Gohler, A.K.Kosfeld, A.Carlton, D.Chiu, H.J.Klock, H.E.Knuth, M.W.Miller, M.D.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Jahreis, K.Wilson, I.A.

(2012) J Bacteriol 194: 2987-2999

  • DOI: https://doi.org/10.1128/JB.00038-12
  • Primary Citation of Related Structures:  
    3DL1, 3KHI

  • PubMed Abstract: 

    MtfA of Escherichia coli (formerly YeeI) was previously identified as a regulator of the phosphoenolpyruvate (PEP)-dependent:glucose phosphotransferase system. MtfA homolog proteins are highly conserved, especially among beta- and gammaproteobacteria. We determined the crystal structures of the full-length MtfA apoenzyme from Klebsiella pneumoniae and its complex with zinc (holoenzyme) at 2.2 and 1.95 Å, respectively. MtfA contains a conserved H(149)E(150)XXH(153)+E(212)+Y(205) metallopeptidase motif. The presence of zinc in the active site induces significant conformational changes in the region around Tyr205 compared to the conformation of the apoenzyme. Additionally, the zinc-bound MtfA structure is in a self-inhibitory conformation where a region that was disordered in the unliganded structure is now observed in the active site and a nonproductive state of the enzyme is formed. MtfA is related to the catalytic domain of the anthrax lethal factor and the Mop protein involved in the virulence of Vibrio cholerae, with conservation in both overall structure and in the residues around the active site. These results clearly provide support for MtfA as a prototypical zinc metallopeptidase (gluzincin clan).


  • Organizational Affiliation

    Joint Center for Structural Genomics, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Metal-dependent Hydrolase267Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: YP_001336084.1mtfAKPN78578_23930KPN_02432
UniProt
Find proteins for A6TB83 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TB83 
Go to UniProtKB:  A6TB83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TB83
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.05α = 90
b = 131.05β = 90
c = 37.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-05-23
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2023-02-01
    Changes: Database references, Derived calculations