3VMA

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3VMA/pdb
Entry: 3VMA supersedes: 3FWM

Classification: TRANSFERASE, HYDROLASE/ANTIBIOTIC
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2011-12-09 Released: 2012-03-14
Deposition Author(s): Huang, C.Y., Sung, M.T., Lai, Y.T., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.250
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.

Sung, M.T., Lai, Y.T., Huang, C.Y., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.

(2009) Proc Natl Acad Sci U S A 106: 8824-8829

PubMed: 19458048 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0904030106
Primary Citation of Related Structures:
3FWL, 3VMA

PubMed Abstract:
Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the development of new antibiotics. Here, we determined the X-ray crystal structure of the bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli in complex with its inhibitor moenomycin to 2.16-A resolution. In addition to the transglycosylase and transpeptidase domains, our structure provides a complete visualization of this important antibacterial target, and reveals a domain for protein-protein interaction and a transmembrane helix domain essential for substrate binding, enzymatic activity, and membrane orientation.

Organizational Affiliation

Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115, Taiwan.

Macromolecule Content

Total Structure Weight: 87.16 kDa
Atom Count: 5,855
Modelled Residue Count: 708
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 1B	A	768	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0149, JW0145, mrcB, pbpF, ponB EC: 2.4.1.129 (PDB Primary Data), 3.4 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P02919 (Escherichia coli (strain K12)) Explore P02919 Go to UniProtKB: P02919
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02919
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M0E Query on M0E Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MOENOMYCIN C₆₉ H₁₀₆ N₅ O₃₄ P NXPRJQIAIORCGO-ZLPAOQQDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.250
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.9	α = 90
b = 289.53	β = 90
c = 62.78	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

This entry supersedes: 3FWM

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description