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PDBsum entry 2p9t

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protein ligands links
Transferase PDB id
2p9t
Jmol
Contents
Protein chain
413 a.a. *
Ligands
3PG
Waters ×289
* Residue conservation analysis
PDB id:
2p9t
Name: Transferase
Title: Crystal structure of phosphoglycerate kinase-2 bound to 3- phosphoglycerate
Structure: Phosphoglycerate kinase, testis specific. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: c3h/he. Gene: pgk2, pgk-2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.221     R-free:   0.269
Authors: G.M.Sawyer,A.F.Monzingo,E.C.Poteet,J.D.Robertus
Key ref:
G.M.Sawyer et al. (2008). X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus. Proteins, 71, 1134-1144. PubMed id: 18004764 DOI: 10.1002/prot.21801
Date:
26-Mar-07     Release date:   27-Nov-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09041  (PGK2_MOUSE) -  Phosphoglycerate kinase 2
Seq:
Struc:
417 a.a.
413 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.2.3  - Phosphoglycerate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Calvin Cycle (carbon fixation stages)
      Reaction: ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
ATP
+
3-phospho-D-glycerate
Bound ligand (Het Group name = 3PG)
corresponds exactly
= ADP
+ 3-phospho-D-glyceroyl phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     flagellar fibrous sheath   4 terms 
  Biological process     sperm motility   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.21801 Proteins 71:1134-1144 (2008)
PubMed id: 18004764  
 
 
X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus.
G.M.Sawyer, A.F.Monzingo, E.C.Poteet, D.A.O'Brien, J.D.Robertus.
 
  ABSTRACT  
 
Phosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X-linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3-phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 A resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the "open" form; that is the N-terminal domain that can bind 3PG and the C-terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13 degree rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C-terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Electron density maps. Electron density from SIGMAA-weighted[39] 2Fo-Fc maps are shown for the (a) unliganded PGK2; (b) the PGK2/3PG complex, showing 3PG and amino acid residues it contacts; (c) the PGK2/ATP complex, showing ATP and nearby protein residues. These stereo maps are contoured at 1.0 .
Figure 2.
Figure 2. PGK2 structure. (a) Ribbon drawing of PGK2. The positions of bound 3PG and ATP are shown with red bonds. Helix 13, which becomes ordered by the binding of 3PG or ATP, is shown in yellow. Secondary structural elements discussed in the text are labeled. (b) Overlay of unliganded PGK2 (open) and the PGK2/3PG (partially closed) complex. The C-terminal domains of the two structures are superimposed by least squares minimization of equivalent C positions. Unliganded PGK2 is represented as a yellow coil, and 3PG-bound PGK2 as a cyan coil. 3PG is shown in cyan bonds. (c) Overlay of the PGK2/3PG and T. brucei PGK/3PG/ATP (closed) complexes.[30] Again, the C-terminal domains of the two structures are superimposed by least squares minimization of equivalent C positions. The PGK2/3PG complex is shown in cyan. The T. brucei ternary complex, with ADP and 3PG bound, is shown in red.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 1134-1144) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19759366 P.V.Danshina, C.B.Geyer, Q.Dai, E.H.Goulding, W.D.Willis, G.B.Kitto, J.R.McCarrey, E.M.Eddy, and D.A.O'Brien (2010).
Phosphoglycerate kinase 2 (PGK2) is essential for sperm function and male fertility in mice.
  Biol Reprod, 82, 136-145.  
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