2H4L | pdb_00002h4l

Complex of PMM/PGM with ribose 1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb2H4L/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-05-24 Released: 2006-08-08 
• Deposition Author(s): Beamer, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor.

Regni, C., Shackelford, G.S., Beamer, L.J.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 722-726

• PubMed: 16880541 
• DOI: https://doi.org/10.1107/S1744309106025887
• Primary Citation Related Structures: 
  2H4L, 2H5A


• PubMed Abstract: 
  

  Two complexes of the enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa with a slow substrate and with an inhibitor have been characterized by X-ray crystallography. Both ligands induce an interdomain rearrangement in the enzyme that creates a highly buried active site. Comparisons with enzyme-substrate complexes show that the inhibitor xylose 1-phosphate utilizes many of the previously observed enzyme-ligand interactions. In contrast, analysis of the ribose 1-phosphate complex reveals a combination of new and conserved enzyme-ligand interactions for binding. The ability of PMM/PGM to accommodate these two pentose phosphosugars in its active site may be relevant for future efforts towards inhibitor design.

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Organizational Affiliation: 
• Department of Structural Biology, St Jude Children's Research Hospital, 332 North Lauderdale M/S 311, Memphis, TN 38105, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.75 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 455 
• Deposited Residue Count: 463 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomannomutase/phosphoglucomutase	A [auth X]	463	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: algC EC: 5.4.2.8 (PDB Primary Data), 5.4.2.2 (PDB Primary Data)
UniProt
Find proteins for P26276 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P26276  Go to UniProtKB:  P26276

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R1P	B [auth X]	1-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P YXJDFQJKERBOBM-TXICZTDVSA-N
ZN	C [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth X]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.717	α = 90
b = 74.095	β = 90
c = 84.347	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Beamer, L.J.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary