3DL1 | pdb_00003dl1

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 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3DL1

This is version 1.6 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 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.

Macromolecule Content 

  • Total Structure Weight: 30.71 kDa 
  • Atom Count: 1,778 
  • Modeled Residue Count: 210 
  • Deposited Residue Count: 267 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
EC: 3.4.11
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
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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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 41 21 2
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
  • Version 1.6: 2024-10-30
    Changes: Data collection, Structure summary