4EHC | pdb_00004ehc

Crystal structure of the C-terminal domain of Rv0977 of Mycobacterium tuberculosis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.213 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.165 (Depositor) 
  • R-Value Observed: 
    0.167 (Depositor) 

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This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16

Barathy, D.V., Suguna, K.

(2013) FEBS Open Bio 3: 256-262

  • DOI: https://doi.org/10.1016/j.fob.2013.05.004
  • Primary Citation Related Structures: 
    4EHC

  • PubMed Abstract: 

    We report the crystal structure of the first prokaryotic aspartic proteinase-like domain identified in the genome of Mycobacterium tuberculosis. A search in the genomes of Mycobacterium species showed that the C-terminal domains of some of the PE family proteins contain two classic DT/SG motifs of aspartic proteinases with a low overall sequence similarity to HIV proteinase. The three-dimensional structure of one of them, Rv0977 (PE_PGRS16) of M. tuberculosis revealed the characteristic pepsin-fold and catalytic site architecture. However, the active site was completely blocked by the N-terminal His-tag. Surprisingly, the enzyme was found to be inactive even after the removal of the N-terminal His-tag. A comparison of the structure with pepsins showed significant differences in the critical substrate binding residues and in the flap tyrosine conformation that could contribute to the lack of proteolytic activity of Rv0977.

    • Organizational Affiliation: 
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content 

  • Total Structure Weight: 32.27 kDa 
  • Atom Count: 2,304 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 296 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PE-PGRS FAMILY PROTEIN296Mycobacterium tuberculosisMutation(s): 0 
Gene Names: PE_PGRS16, Rv0977
UniProt
Find proteins for Q79FU3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q79FU3 
Go to UniProtKB:  Q79FU3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79FU3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN


Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
C [auth A]
CA [auth A]
D [auth A]
AA [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
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: 1.98 Å
  • R-Value Free:  0.213 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.165 (Depositor) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.11α = 90
b = 66.16β = 90
c = 69.62γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
Auto-Rickshawphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary