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PDBsum entry 1s2u

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1s2u
Jmol
Contents
Protein chains
290 a.a. *
Ligands
PEG ×2
Waters ×568
* Residue conservation analysis
PDB id:
1s2u
Name: Isomerase
Title: Crystal structure of the d58a phosphoenolpyruvate mutase mut protein
Structure: Phosphoenolpyruvate phosphomutase. Chain: a, b. Synonym: phosphoenolpyruvate mutase, pep mutase, pep phosph engineered: yes. Mutation: yes
Source: Mytilus edulis. Organism_taxid: 6550. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.165     R-free:   0.219
Authors: S.Liu,Z.Lu,Y.Han,Y.Jia,A.Howard,D.Dunaway-Mariano,O.Herzberg
Key ref:
S.Liu et al. (2004). Conformational flexibility of PEP mutase. Biochemistry, 43, 4447-4453. PubMed id: 15078090 DOI: 10.1021/bi036255h
Date:
11-Jan-04     Release date:   04-May-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56839  (PEPM_MYTED) -  Phosphoenolpyruvate phosphomutase
Seq:
Struc:
295 a.a.
290 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.4.2.9  - Phosphoenolpyruvate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Phosphoenolpyruvate Mutase
      Reaction: Phosphoenolpyruvate = 3-phosphonopyruvate
Phosphoenolpyruvate
= 3-phosphonopyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     organic phosphonate biosynthetic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi036255h Biochemistry 43:4447-4453 (2004)
PubMed id: 15078090  
 
 
Conformational flexibility of PEP mutase.
S.Liu, Z.Lu, Y.Han, Y.Jia, A.Howard, D.Dunaway-Mariano, O.Herzberg.
 
  ABSTRACT  
 
Previous work has indicated that PEP mutase catalyzes the rearrangement of phosphoenolpyruvate to phosphonopyruvate by a dissociative mechanism. The crystal structure of the mutase with Mg(II) and sulfopyruvate (a phosphonopyruvate analogue) bound showed that the substrate is anchored to the active site by the Mg(II), and shielded from solvent by a large loop (residues 115-133). Here, the crystal structures of wild-type and D58A mutases, in the apo state and in complex with Mg(II), are reported. In both unbound and Mg(II)-bound states, the active site is accessible to the solvent. The loop (residues 115-133), which in the enzyme-inhibitor complexes covers the active site cavity, is partially disordered or adopts a conformation that allows access to the cavity. In the apo state, the residues associated with Mg(II) binding are poised to accept the metal ion. When Mg(II) binds, the coordination is the same as that previously observed in the enzyme-Mg(II) sulfopyruvate complex, except that the coordination positions occupied by two ligand oxygen atoms are occupied by two water molecules. When the loop opens, three key active site residues are displaced from the active site, Lys120, Asn122, and Leu124. Lys120 mediates Mg(II) coordination. Asn122 and Leu124 surround the transferring phosphoryl group, and thus prevent substrate hydrolysis. Amino acid replacement of any one of these three loop residues results in a significant loss of catalytic activity. It is hypothesized that the loop serves to gate the mutase active site, interconverting between an open conformation that allows substrate binding and product release and a closed conformation that separates the reaction site from the solvent during catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18081320 B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, and O.Herzberg (2008).
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
  Biochemistry, 47, 167-182.
PDB code: 3b8i
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
17283804 I.Ntai, V.V.Phelan, and B.O.Bachmann (2006).
Phosphonopeptide K-26 biosynthetic intermediates in Astrosporangium hypotensionis.
  Chem Commun (Camb), (), 4518-4520.  
17124494 M.Kato, R.M.Wynn, J.L.Chuang, C.A.Brautigam, M.Custorio, and D.T.Chuang (2006).
A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.
  EMBO J, 25, 5983-5994.
PDB codes: 2ihw 2ii3 2ii4 2ii5
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 code is shown on the right.