6W4Q

Crystal structure of full-length tailspike protein 2 (TSP2, ORF211) ) from Escherichia coli O157:H7 bacteriophage CAB120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7.

Greenfield, J.Shang, X.Luo, H.Zhou, Y.Linden, S.B.Heselpoth, R.D.Leiman, P.G.Nelson, D.C.Herzberg, O.

(2020) Sci Rep 10: 15402-15402

  • DOI: https://doi.org/10.1038/s41598-020-72373-0
  • Primary Citation of Related Structures:  
    6W4Q

  • PubMed Abstract: 

    The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.


  • Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Dr, Rockville, MD, 20850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tail fiber
A, B, C, D, E
A, B, C, D, E, F
927Kuttervirus CBA120Mutation(s): 0 
Gene Names: orf211
UniProt
Find proteins for G3M190 (Escherichia phage Cba120)
Explore G3M190 
Go to UniProtKB:  G3M190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3M190
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AD [auth E]
EA [auth A]
FA [auth A]
GA [auth A]
GB [auth B]
AD [auth E],
EA [auth A],
FA [auth A],
GA [auth A],
GB [auth B],
HB [auth B],
HC [auth C],
IB [auth B],
IC [auth C],
ID [auth E],
JC [auth C],
JD [auth E],
KD [auth E],
LA [auth A],
MB [auth C],
NA [auth A],
PA [auth B],
PC [auth D],
PD [auth F],
QC [auth D],
QD [auth F],
RD [auth F],
SD [auth F],
YC [auth D],
ZC [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth C]
BA [auth A]
BB [auth B]
AA [auth A],
AB [auth B],
AC [auth C],
BA [auth A],
BB [auth B],
BC [auth C],
BD [auth E],
CA [auth A],
CB [auth B],
CC [auth C],
CD [auth E],
DA [auth A],
DB [auth B],
DC [auth C],
DD [auth E],
EB [auth B],
EC [auth C],
ED [auth E],
FB [auth B],
FC [auth C],
FD [auth E],
G [auth A],
GC [auth C],
GD [auth E],
H [auth A],
HD [auth E],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
LB [auth C],
LD [auth F],
M [auth A],
MA [auth A],
MD [auth F],
N [auth A],
NB [auth C],
NC [auth D],
ND [auth F],
O [auth A],
OB [auth C],
OC [auth D],
OD [auth F],
P [auth A],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
R [auth A],
RA [auth B],
RB [auth C],
S [auth A],
SA [auth B],
SB [auth C],
T [auth A],
TA [auth B],
TB [auth C],
U [auth A],
UA [auth B],
UB [auth C],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth D],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth D],
Y [auth A],
YA [auth B],
YB [auth C],
Z [auth A],
ZA [auth B],
ZB [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
KB [auth B],
KC [auth C],
LC [auth C],
MC [auth C],
OA [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
KA [auth A],
TC [auth D]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
HA [auth A]
IA [auth A]
JA [auth A]
JB [auth B]
RC [auth D]
HA [auth A],
IA [auth A],
JA [auth A],
JB [auth B],
RC [auth D],
SC [auth D],
UC [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.992α = 90
b = 259.009β = 90
c = 269.696γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM110202

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description