2AIZ | pdb_00002aiz

Solution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine

• PDB DOI: https://doi.org/10.2210/pdb2AIZ/pdb
• BMRB: 6858
• BMRB: 6465
• BMRB: 6856

• Classification: MEMBRANE PROTEIN
• Organism(s): Haemophilus influenzae, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-01 Released: 2006-03-14 
• Deposition Author(s): Parsons, L.M., Lin, F., Orban, J., Structure 2 Function Project (S2F)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Peptidoglycan recognition by pal, an outer membrane lipoprotein.

Parsons, L.M., Lin, F., Orban, J.

(2006) Biochemistry 45: 2122-2128

• PubMed: 16475801 
• DOI: https://doi.org/10.1021/bi052227i
• Primary Citation Related Structures: 
  2AIZ


• PubMed Abstract: 
  

  Peptidoglycan-associated lipoprotein (Pal) is a potential vaccine candidate from Haemophilus influenzae that is highly conserved in Gram-negative bacteria and anchored to the outer membrane through an N-terminal lipid attachment. Pal stabilizes the outer membrane by providing a noncovalent link to the peptidoglycan (PG) layer through a periplasmic domain. Using NMR spectroscopy, we determined the three-dimensional structure of a complex between the periplasmic domain of Pal and a biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-alpha-d-Glu-m-Dap-D-Ala-d-Ala (m-Dap is meso-diaminopimelate). Pal has a binding pocket lined with conserved surface residues that interacts exclusively with the peptide portion of the ligand. The m-Dap residue, which is mainly found in the cell walls of Gram-negative bacteria, is sequestered in this pocket and plays an important role by forming hydrogen bond and hydrophobic contacts to Pal. The structure provides insight into the mode of cell wall recognition for a broad class of Gram-negative membrane proteins, including OmpA and MotB, which have peptidoglycan-binding domains homologous to that of Pal.

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Organizational Affiliation: 
• Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.48 kDa 
• Atom Count: 1,086 
• Modeled Residue Count: 139 
• Deposited Residue Count: 139 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein P6 (Fragment)	A [auth P]	134	Haemophilus influenzae	Mutation(s): 0  Gene Names: ompP6
UniProt
Find proteins for P10324 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P10324  Go to UniProtKB:  P10324

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine	B [auth U]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	D [auth U]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
AMU	C [auth U]	N-acetyl-beta-muramic acid C11 H19 N O8 MNLRQHMNZILYPY-YVNCZSHWSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6CL	B [auth U]	L-PEPTIDE LINKING	C7 H15 N2 O4		LYS
DAL	B [auth U]	D-PEPTIDE LINKING	C3 H7 N O2		--
DGL	B [auth U]	D-PEPTIDE LINKING	C5 H9 N O4		--

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Parsons, L.M., Lin, F., Orban, J., Structure 2 Function Project (S2F)

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.0: 2023-02-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Structure summary