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 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    3G0T

  • 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 prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative aminotransferaseA, B437Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: NP_905498.1, PG_1327
UniProt
Find proteins for Q7MUZ3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MUZ3 
Go to UniProtKB:  Q7MUZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MUZ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4
Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B]		2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
AA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
P [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP		A, B L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.44α = 90
b = 54.97β = 90
c = 81.154γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description