6OAD

2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Currently 6OAD does not have a validation slider image.


This is version 1.4 of the entry. See complete history


Literature

Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.

Minasov, G.Lam, M.R.Rosas-Lemus, M.Slawek, J.Woinska, M.Shabalin, I.G.Shuvalova, L.Palsson, B.O.Godzik, A.Minor, W.Satchell, K.J.F.

(2020) Protein Sci 29: 1618-1628

  • DOI: https://doi.org/10.1002/pro.3876
  • Primary Citation of Related Structures:  
    6OAD, 6OV8

  • PubMed Abstract: 

    Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn 2+ and Mn 2+ , while the second structure has two Zn 2+ ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.


  • Organizational Affiliation

    Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase B
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
430Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: pepBD8B36_06045
EC: 3.4.11.23
UniProt
Find proteins for P37095 (Escherichia coli (strain K12))
Explore P37095 
Go to UniProtKB:  P37095
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37095
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
U [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
GB [auth E],
LA [auth C],
QD [auth L],
WA [auth D],
XA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AD [auth K]
BD [auth K]
DA [auth C]
EA [auth C]
HB [auth F]
AD [auth K],
BD [auth K],
DA [auth C],
EA [auth C],
HB [auth F],
IB [auth F],
IC [auth I],
ID [auth L],
JC [auth I],
JD [auth L],
M [auth A],
N [auth A],
NA [auth D],
OA [auth D],
QB [auth G],
RB [auth G],
RC [auth J],
SC [auth J],
V [auth B],
W [auth B],
YA [auth E],
YB [auth H],
ZA [auth E],
ZB [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CC [auth H]
DB [auth E]
DC [auth H]
AA [auth B],
BA [auth B],
CC [auth H],
DB [auth E],
DC [auth H],
EB [auth E],
EC [auth H],
FB [auth E],
FC [auth H],
GC [auth H],
GD [auth K],
HC [auth H],
HD [auth K],
JA [auth C],
KA [auth C],
MA [auth C],
NB [auth F],
OB [auth F],
OC [auth I],
OD [auth L],
PB [auth F],
PC [auth I],
PD [auth L],
QC [auth I],
R [auth A],
RD [auth L],
S [auth A],
T [auth A],
TA [auth D],
UA [auth D],
VA [auth D],
VB [auth G],
VC [auth J],
WB [auth G],
WC [auth J],
XB [auth G],
XC [auth J],
YC [auth J],
ZC [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
BC [auth H]
CB [auth E]
ED [auth K]
FD [auth K]
HA [auth C]
BC [auth H],
CB [auth E],
ED [auth K],
FD [auth K],
HA [auth C],
IA [auth C],
LB [auth F],
MB [auth F],
MC [auth I],
NC [auth I],
ND [auth L],
Q [auth A],
QA [auth D],
RA [auth D],
SA [auth D],
TB [auth G],
UB [auth G],
UC [auth J],
Z [auth B]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth E]
AC [auth H]
CD [auth K]
FA [auth C]
JB [auth F]
AB [auth E],
AC [auth H],
CD [auth K],
FA [auth C],
JB [auth F],
KC [auth I],
KD [auth L],
LC [auth I],
O [auth A],
PA [auth D],
SB [auth G],
TC [auth J],
X [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth E]
CA [auth B]
DD [auth K]
GA [auth C]
KB [auth F]
BB [auth E],
CA [auth B],
DD [auth K],
GA [auth C],
KB [auth F],
LD [auth L],
MD [auth L],
P [auth A],
Y [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.667α = 90
b = 114.761β = 92.02
c = 161.171γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing

Structure Validation

View Full Validation Report

Currently 6OAD does not have a validation slider image.



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Refinement description
  • Version 1.2: 2021-01-27
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-04-07
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description