Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.87 kDa 
• Atom Count: 3577 
• Modelled Residue Count: 428 
• Deposited Residue Count: 437 
• Unique protein chains: 1

1UAG

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

• PDB DOI: 10.2210/pdb1UAG/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-03-13 Released: 1998-03-18 
• Deposition Author(s): Bertrand, J., Fanchon, E., Dideberg, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.

Bertrand, J.A., Auger, G., Fanchon, E., Martin, L., Blanot, D., van Heijenoort, J., Dideberg, O.

(1997) EMBO J 16: 3416-3425

• PubMed: 9218784 
• DOI: 10.1093/emboj/16.12.3416
• Primary Citation of Related Structures:  
  1UAG


• PubMed Abstract: 
  

UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal structure of MurD in the presence of its substrate UMA has been solved to 1.9 A resolution. Phase information was obtained from multiple anomalous dispersion using the K-shell edge of selenium in combination with multiple isomorphous replacement. The structure comprises three domains of topology each reminiscent of nucleotide-binding folds: the N- and C-terminal domains are consistent with the dinucleotide-binding fold called the Rossmann fold, and the central domain with the mononucleotide-binding fold also observed in the GTPase family. The structure reveals the binding site of the substrate UMA, and comparison with known NTP complexes allows the identification of residues interacting with ATP. The study describes the first structure of the UDP-N-acetylmuramoyl-peptide ligase family.

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Organizational Affiliation: 

Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), Laboratoire de Cristallographie Macromoléculaire, Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYL-L-ALANINE/:D-GLUTAMATE LIGASE	A	437	Escherichia coli	Mutation(s): 1  Gene Names: MURD GENE EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900  Go to UniProtKB:  P14900

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMA	D [auth A]	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE C23 H36 N4 O20 P2 NTMMCWJNQNKACG-KBKUWGQMSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.428	α = 90
b = 65.428	β = 90
c = 134.438	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MADSYS	phasing
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-03-13 
• Released Date: 1998-03-18 
Deposition Author(s): Bertrand, J., Fanchon, E., Dideberg, O.

Revision History  

• Version 1.0: 1998-03-18
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2018-04-11
  Changes: Data collection