8WT1

Crystal structure of S9 carboxypeptidase from Geobacillus sterothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity.

Chandravanshi, K.Singh, R.Bhange, G.N.Kumar, A.Yadav, P.Kumar, A.Makde, R.D.

(2024) FEBS Lett 598: 684-701

  • DOI: https://doi.org/10.1002/1873-3468.14834
  • Primary Citation of Related Structures:  
    8WT1

  • PubMed Abstract: 

    Acylaminoacyl peptidases (AAPs) play a pivotal role in various pathological conditions and are recognized as potential therapeutic targets. AAPs exhibit a wide range of activities, such as acylated amino acid-dependent aminopeptidase, endopeptidase, and less studied carboxypeptidase activity. We have determined the crystal structure of an AAP from Geobacillus stearothermophilus (S9gs) at 2.0 Å resolution. Despite being annotated as an aminopeptidase in the NCBI database, our enzymatic characterization proved S9gs to be a carboxypeptidase. Solution-scattering studies showed that S9gs exists as a tetramer in solution, and crystal structure analysis revealed adaptations responsible for the carboxypeptidase activity of S9gs. The findings present a hypothesis for substrate selection, substrate entry, and product exit from the active site, enriching our understanding of this rare carboxypeptidase.


  • Organizational Affiliation

    Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S9 family peptidase
A, B, C, D, E
A, B, C, D, E, F, G, H
691Geobacillus stearothermophilus ATCC 12980Mutation(s): 0 
Gene Names: D9548_14720
UniProt
Find proteins for A0A3L7D5Q2 (Geobacillus stearothermophilus)
Explore A0A3L7D5Q2 
Go to UniProtKB:  A0A3L7D5Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L7D5Q2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC (Subject of Investigation/LOI)
Query on FLC

Download Ideal Coordinates CCD File 
QD [auth H],
Y [auth A]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
AC [auth E]
BA [auth B]
BC [auth E]
CA [auth B]
AA [auth B],
AC [auth E],
BA [auth B],
BC [auth E],
CA [auth B],
DA [auth B],
EA [auth B],
ED [auth H],
FA [auth B],
FB [auth D],
FD [auth H],
GA [auth B],
GB [auth D],
GD [auth H],
HA [auth B],
HB [auth D],
HD [auth H],
I [auth A],
IA [auth B],
IB [auth D],
IC [auth F],
ID [auth H],
J [auth A],
JA [auth B],
JB [auth D],
JC [auth F],
JD [auth H],
K [auth A],
KA [auth B],
KB [auth D],
KC [auth F],
KD [auth H],
L [auth A],
LB [auth D],
LC [auth F],
LD [auth H],
M [auth A],
MB [auth D],
MC [auth F],
MD [auth H],
N [auth A],
NC [auth F],
O [auth A],
OC [auth F],
P [auth A],
SA [auth C],
TA [auth C],
TB [auth E],
UA [auth C],
UB [auth E],
VA [auth C],
VB [auth E],
VC [auth G],
WA [auth C],
WB [auth E],
WC [auth G],
XA [auth C],
XB [auth E],
XC [auth G],
YA [auth C],
YB [auth E],
YC [auth G],
Z [auth B],
ZB [auth E],
ZC [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
BD [auth G]
CB [auth C]
CD [auth G]
AB [auth C],
BB [auth C],
BD [auth G],
CB [auth C],
CD [auth G],
DB [auth C],
EC [auth E],
FC [auth E],
GC [auth E],
OB [auth D],
OD [auth H],
PA [auth B],
PB [auth D],
PC [auth F],
QA [auth B],
QB [auth D],
QC [auth F],
RB [auth D],
RC [auth F],
SC [auth F],
TC [auth F],
U [auth A],
V [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA
Query on ALA

Download Ideal Coordinates CCD File 
DD [auth G]
EB [auth C]
HC [auth E]
PD [auth H]
RA [auth B]
DD [auth G],
EB [auth C],
HC [auth E],
PD [auth H],
RA [auth B],
SB [auth D],
UC [auth F],
X [auth A]
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
AD [auth G]
CC [auth E]
DC [auth E]
LA [auth B]
MA [auth B]
AD [auth G],
CC [auth E],
DC [auth E],
LA [auth B],
MA [auth B],
NA [auth B],
NB [auth D],
ND [auth H],
OA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
ZA [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.123α = 90
b = 75.443β = 93.27
c = 219.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science & Technology (DST, India)IndiaIF190153

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references