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PDBsum entry 1p5d

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protein ligands metals links
Isomerase PDB id
1p5d
Jmol
Contents
Protein chain
455 a.a. *
Ligands
G1P
Metals
_ZN
Waters ×464
* Residue conservation analysis
PDB id:
1p5d
Name: Isomerase
Title: Enzyme-ligand complex of p. Aeruginosa pmm/pgm
Structure: Phosphomannomutase. Chain: x. Synonym: pmm. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Gene: algc or pa5322. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.157     R-free:   0.179
Authors: C.Regni,P.A.Tipton,L.J.Beamer
Key ref:
C.Regni et al. (2004). Structural basis of diverse substrate recognition by the enzyme PMM/PGM from P. aeruginosa. Structure, 12, 55-63. PubMed id: 14725765 DOI: 10.1016/j.str.2003.11.015
Date:
25-Apr-03     Release date:   20-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26276  (ALGC_PSEAE) -  Phosphomannomutase/phosphoglucomutase
Seq:
Struc:
463 a.a.
455 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.5.4.2.2  - Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
UDP-glucose, UDP-galactose and UDP-glucuronate Biosynthesis
      Reaction: Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate
Alpha-D-glucose 1-phosphate
Bound ligand (Het Group name = G1P)
corresponds exactly
= alpha-D-glucose 6-phosphate
   Enzyme class 2: E.C.5.4.2.8  - Phosphomannomutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: Alpha-D-mannose 1-phosphate = D-mannose 6-phosphate
Alpha-D-mannose 1-phosphate
Bound ligand (Het Group name = G1P)
corresponds exactly
= D-mannose 6-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2003.11.015 Structure 12:55-63 (2004)
PubMed id: 14725765  
 
 
Structural basis of diverse substrate recognition by the enzyme PMM/PGM from P. aeruginosa.
C.Regni, L.Naught, P.A.Tipton, L.J.Beamer.
 
  ABSTRACT  
 
Enzyme-substrate complexes of phosphomannomutase/phosphoglucomutase (PMM/PGM) reveal the structural basis of the enzyme's ability to use four different substrates in catalysis. High-resolution structures with glucose 1-phosphate, glucose 6-phosphate, mannose 1-phosphate, and mannose 6-phosphate show that the position of the phosphate group of each substrate is held constant by a conserved network of hydrogen bonds. This produces two distinct, and mutually exclusive, binding orientations for the sugar rings of the 1-phospho and 6-phospho sugars. Specific binding of both orientations is accomplished by key contacts with the O3 and O4 hydroxyls of the sugar, which must occupy equatorial positions. Dual recognition of glucose and mannose phosphosugars uses a combination of specific protein contacts and nonspecific solvent contacts. The ability of PMM/PGM to accommodate these four diverse substrates in a single active site is consistent with its highly reversible phosphoryl transfer reaction and allows it to function in multiple biosynthetic pathways in P. aeruginosa.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Mechanism and Overall Structure of PMM/PGM(A) Mechanism of PMM/PGM shown in the biosynthetic direction of the reaction with G6P as the substrate.(B) Tube rendering of PMM/PGM and the G1P complex. The apo-protein and G1P complex were superimposed, and the areas differing between the two protein backbones are shown as a tube of varying diameter, proportional to the differences between the two structures. Domains 1 to 4 are shown in green (residues 1-153), yellow (residues 154-256), red (residues 257-368), and blue (residues 369-463), respectively.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 55-63) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20512975 A.M.Schramm, D.Karr, R.Mehra-Chaudhary, S.R.Van Doren, C.M.Furdui, and L.J.Beamer (2010).
Breaking the covalent connection: Chain connectivity and the catalytic reaction of PMM/PGM.
  Protein Sci, 19, 1235-1242.  
20589904 G.Y.Chuang, R.Mehra-Chaudhary, C.H.Ngan, B.S.Zerbe, D.Kozakov, S.Vajda, and L.J.Beamer (2010).
Domain motion and interdomain hot spots in a multidomain enzyme.
  Protein Sci, 19, 1662-1672.  
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
18824121 L.Nic Lochlainn, and P.Caffrey (2009).
Phosphomannose isomerase and phosphomannomutase gene disruptions in Streptomyces nodosus: impact on amphotericin biosynthesis and implications for glycosylation engineering.
  Metab Eng, 11, 40-47.  
16595672 C.Regni, A.M.Schramm, and L.J.Beamer (2006).
The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme.
  J Biol Chem, 281, 15564-15571.
PDB codes: 2fkf 2fkm
  16880541 C.Regni, G.S.Shackelford, and L.J.Beamer (2006).
Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 722-726.
PDB codes: 2h4l 2h5a
15813726 D.M.Ramsey, and D.J.Wozniak (2005).
Understanding the control of Pseudomonas aeruginosa alginate synthesis and the prospects for management of chronic infections in cystic fibrosis.
  Mol Microbiol, 56, 309-322.  
16209952 D.R.Ronning, C.Guynet, B.Ton-Hoang, Z.N.Perez, R.Ghirlando, M.Chandler, and F.Dyda (2005).
Active site sharing and subterminal hairpin recognition in a new class of DNA transposases.
  Mol Cell, 20, 143-154.
PDB codes: 2a6m 2a6o
15889412 K.Hirotsu, M.Goto, A.Okamoto, and I.Miyahara (2005).
Dual substrate recognition of aminotransferases.
  Chem Rec, 5, 160-172.  
16313562 N.Kato, C.R.Mueller, V.Wessely, Q.Lan, and B.M.Christensen (2005).
Aedes aegypti phosphohexomutases and uridine diphosphate-hexose pyrophosphorylases: comparison of primary sequences, substrate specificities and temporal transcription.
  Insect Mol Biol, 14, 615-624.  
15937189 W.K.Ray, S.M.Keith, A.M.DeSantis, J.P.Hunt, T.J.Larson, R.F.Helm, and P.J.Kennelly (2005).
A phosphohexomutase from the archaeon Sulfolobus solfataricus is covalently modified by phosphorylation on serine.
  J Bacteriol, 187, 4270-4275.  
15238632 G.S.Shackelford, C.A.Regni, and L.J.Beamer (2004).
Evolutionary trace analysis of the alpha-D-phosphohexomutase superfamily.
  Protein Sci, 13, 2130-2138.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.