3G0T

Crystal structure of putative aspartate aminotransferase (NP_905498.1) from Porphyromonas gingivalis W83 at 1.75 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.

Fleischman, N.M.Das, D.Kumar, A.Xu, Q.Chiu, H.J.Jaroszewski, L.Knuth, M.W.Klock, H.E.Miller, M.D.Elsliger, M.A.Godzik, A.Lesley, S.A.Deacon, A.M.Wilson, I.A.Toney, M.D.

(2014) Protein Sci. 23: 1060-1076

  • DOI: 10.1002/pro.2493

  • PubMed Abstract: 
  • Pyridoxal-5'-phosphate or PLP, the active form of vitamin B6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. PLP-dependent enzymes account for ∼1.5% of most proka ...

    Pyridoxal-5'-phosphate or PLP, the active form of vitamin B6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. PLP-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. Here, we structurally and functionally characterize three novel PLP-dependent enzymes from bacteria in the human microbiome: two are from Eubacterium rectale, a dominant, nonpathogenic, fecal, Gram-positive bacteria, and the third is from Porphyromonas gingivalis, which plays a major role in human periodontal disease. All adopt the Type I PLP-dependent enzyme fold and structure-guided biochemical analysis enabled functional assignments as tryptophan, aromatic, and probable phosphoserine aminotransferases.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis, California, 95616.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative aminotransferase
A, B
437Porphyromonas gingivalis (strain ATCC BAA-308 / W83)Mutation(s): 0 
Find proteins for Q7MUZ3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  Q7MUZ3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download SDF File 
Download CCD File 
B
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 220.440α = 90.00
b = 54.970β = 90.00
c = 81.154γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
SHELXDphasing
MolProbitymodel building
MAR345data collection
PHENIXrefinement
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-09-24
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence, Refinement description