Motion in Phosphoglycerate Kinase [pgk]

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Classification Known Domain Motion, Hinge Mechanism [D-h-2]

Structures
13PK Closed ternary [ PartsList ]
1PHP Open binary [ PartsList ]
2PGK Open apo

Description
A 32 degree hinge motion with a positional displacement of up to 27 angstrom between open and closed crystal structures is observed. This, and the residue numbering below, refers to the closed trypanosomal structure (13PK). The actual hinge bending motion shown in the movie was modelled by biased molecular dynamics without knowledge of the closed conformation. Key hinge motions were observed but the extent of closing was slightly exaggerated.

Particular values describing motion
Creation Date = 1999-03-31
Domain 1 (residue selection) = 5-194, 411
Domain 2 (residue selection) = 211-394
Location of a Hinge (residue selection) = 195-210, 3
Maximum CA displacement (A) = 27
Maximum Rotation (degrees) = 32
Number of hinges = 2
Modification Date = 1999-04-01 03:49:26.000

References
A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. N.R. Chandra, H. Muirhead, J.J. Holbrook, B.E. Bernstein, W.G.J. Hol & R.B. Sessions. Proteins 30 (1998) 372-380. [Medline info for 89125622]
Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. B.E. Bernstein, P.A. Michels & W.G.J. Hol. Nature 385 (1997) 275-278. [Medline info for 89125622]

Data and Graphics
Hinge bending movie A GIF animation of the molecular dynamics
Richard B. Sessions Home Page Please contact r.sessions@bris.ac.uk regarding this entry

GO terms associated with structures
Molecular functionphosphoglycerate kinase activity
Biological processglycolysis

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Phosphoglycerate Kin 13pk [ A ] 1php [ A ] 394

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
07465-18127 Phosphoglycerate Kin 13pk [ A ] 1php [ A ] 394
14747-19204 Phosphoglycerate kin upload [ A ] upload [ A ] 407
17289-21085 Phosphoglycerate kin upload [ A ] upload [ A ] 407
89734-5746 Phosphoglycerate kin upload [ A ] upload [ A ] 407
782462-1049 Phosphoglycerate Kinase upload [ A ] upload [ A ] 415
783324-2265 Phosphoglycerate Kinase upload [ A ] upload [ A ] 415

Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va16pkA-13pkC 3-Phosphoglycerate Kinase 16pk [ A ] 13pk [ C ] 415
va16pkA-13pkA 3-Phosphoglycerate Kinase 16pk [ A ] 13pk [ A ] 415
va16pkA-13pkB 3-Phosphoglycerate Kinase 16pk [ A ] 13pk [ B ] 415
va16pkA-13pkD 3-Phosphoglycerate Kinase 16pk [ A ] 13pk [ D ] 415

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu