Motion in Adenylate Kinase (ADK) [adk]

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

Structures
1AK3 Conformation 1
1AKE Conformation 2 [ PartsList ]
1ANK Conformation 3 [ PartsList ]
3ADK Conformation 4 [ PartsList ]

Description
2 interdomain linkages and 4 hinges (one involves kinking helix). 60 degree rotation from 1st pair of hinges, 30 degree from 2nd pair, 90 degree total. In large variants of adenylate kinase the AMP and ATP substrates are buried by a domain rotating by 90 degrees. The mobile domain is linked to the rest of the protein by two helices packed together in an antiparallel fashion. During the closure, deformations take place in four localized regions, called joints, near the N and C termini of these helices. Three of these joints have simple motions that can be well approximated by rotations of three torsion angles, but the joint that makes contact with the ligand involves motion throughout an extended loop: i.e. two torsions on either side of a reverse turn change significantly. The main chain atoms of the joints have few packing constraints. The first pair of joints is responsible for approximately 30 degrees of the total rotation and the second pair for the remaining approximately 60 degrees. These movements carries along the regions between the joints, the two helices and the rest of the mobile domain, to a first approximation, as rigid bodies. ADK also has a shear motion when the first substrate, AMP, binds: i.e. in moving from the conformation of 3ADK to 1AK3, 3 helices with acrossed geometry shift 1-2 Angstroms to rearrange the geometry of the nucleotide binding site slightly.

Particular values describing motion
Creation Date = 19970822
Experimental Methods = x (Traditional x-ray)
Modification Date = 1999-11-04 14:04:40.000

References
G E Schulz, C W Muller and K Diederichs (1990). Induced-fit movement in adenylate kinases. J. Mol. Biol. 213: 627-630. [Medline info for 9615437]
K Diederichs and G E Schulz (1991). Refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 angstrom resolution. J. Mol. Biol. 217: 541-549. [Medline info for 9615437]
M B Berry, B Meador, T Bilderback, P Liang, M Glaser and J G N Phillips (1994). The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins: Struc. Func. Genet. 19: 183-198. [Medline info for 9615437]
M Gerstein, G Schulz and C Chothia (1993). Domain Closure in Adenylate Kinase: Joints on Either Side of Two Helices Close Like Neighboring Fingers. J. Mol. Biol. 229: 494-501. [Medline info for 93156056]

Data and Graphics
Graphic-2 Small shearing motion when the AMP binds (unrelated to major hinge motion).
Graphic-3 The two hinges on either side of helix 7.
Graphic-1 Overall motion.
Adenylate Kinase -- the movie Courtesy of Clemens Vonrhein, Gerd J Schlauderer and Georg E Schulz.

GO terms associated with structures
Molecular functionnucleotide kinase activity, adenylate kinase activity, ATP binding
Cellular componentcytoplasm
Biological processATP metabolism, nucleobase, nucleoside, nucleotide and nucleic acid metabolism

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Via_align 1ake [ A ] 1ank [ A ] 214

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
664460-30963 Adenylate Kinase 1ak3 [ A ] 1ake [ A ] 194
664507-30996 Adenylate Kinase 1ak3 [ A ] 1ake [ A ] 194
672306-3127 Adenylate Kinase 1ak3 [ A ] 1ake [ A ] 214
079851-18092 Adenylate Kinase 1ak2 [ B ] 2ak3 [ B ] 226
079867-18117 Adenylate Kinase 1ak2 [ A ] 2ak3 [ A ] 226
571666-8867 ADENYLATE KINASE upload [ A ] upload [ A ] 226
768686-3676 Adenylate Kinase 1ank [ A ] 4ake [ A ] 214
498099-12557 adenylate kinase 1ake [ A ] 4ake [ A ] 214
812918-15603 adenylate kinase 1ake [ A ] 4ake [ A ] 214
348708-14106 Adenylate Kinase 1ake [ A ] 4ake [ A ] 214
387929-14500 Adenylate kinase AMP movement upload [ A ] upload [ A ] 214
387856-14214 Adenylate kinase ATP movement upload [ A ] upload [ A ] 214
461086-7711 adenylate kinase from E. coli 4ake [ A ] 1ake [ A ] 214
533252-2145 adk upload [ A ] upload [ A ] 214
534229-3259 adk upload [ A ] upload [ A ] 214
534851-4453 adk upload [ A ] upload [ A ] 214
535136-5567 adk upload [ A ] upload [ A ] 214
535962-6743 adk upload [ A ] upload [ A ] 214
536289-7789 adk upload [ A ] upload [ A ] 214
537052-8912 adk upload [ A ] upload [ A ] 214
537329-9991 adk upload [ A ] upload [ A ] 214
541793-12034 adk upload [ A ] upload [ A ] 214
811597-5540 ADK (obsolete PDB en upload [ A ] 1ake [ A ] 214
399385-17776 Adk_AMP upload [ A ] upload [ A ] 214
399445-18086 Adk_ATP upload [ A ] upload [ A ] 214
399305-17495 Adk_full upload [ A ] upload [ A ] 214
74664-1072 Via_align 3adk [ A ] 1ake [ A ] 214

Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va2eckA-4akeA Adenylate Kinase 2eck [ A ] 4ake [ A ] 214
va2eckB-4akeA Adenylate Kinase 2eck [ B ] 4ake [ A ] 214
va4akeA-1e4vB Adenylate Kinase 4ake [ A ] 1e4v [ B ] 214
va4akeA-1e4vA Adenylate Kinase 4ake [ A ] 1e4v [ A ] 214
va2eckA-4akeB Adenylate Kinase 2eck [ A ] 4ake [ B ] 214
va4akeB-2eckB Adenylate Kinase 4ake [ B ] 2eck [ B ] 214
va4akeB-1ankB Adenylate Kinase 4ake [ B ] 1ank [ B ] 214
va4akeB-1akeB Adenylate Kinase 4ake [ B ] 1ake [ B ] 214
va4akeB-1e4vA Adenylate Kinase 4ake [ B ] 1e4v [ A ] 214
va4akeA-1e4yA Adenylate Kinase 4ake [ A ] 1e4y [ A ] 214
va4akeB-1e4yA Adenylate Kinase 4ake [ B ] 1e4y [ A ] 214
va4akeA-1e4yB Adenylate Kinase 4ake [ A ] 1e4y [ B ] 214
va1ankB-4akeA Adenylate Kinase (Adk) (E.C. 2 1ank [ B ] 4ake [ A ] 214
va1ankA-4akeA Adenylate Kinase (Adk) (E.C. 2 1ank [ A ] 4ake [ A ] 214
va1ankA-4akeB Adenylate Kinase (Adk) (E.C. 2 1ank [ A ] 4ake [ B ] 214
va1akeB-4akeA Adenylate Kinase (E.C. 2.7.4.3 1ake [ B ] 4ake [ A ] 214
va1akeA-4akeA Adenylate Kinase (E.C. 2.7.4.3 1ake [ A ] 4ake [ A ] 214
va1akeA-4akeB Adenylate Kinase (E.C. 2.7.4.3 1ake [ A ] 4ake [ B ] 214
va1e4vB-4akeB Mol_Id: 1; Molecule: Adenylate 1e4v [ B ] 4ake [ B ] 214
va1e4yB-4akeB Mol_Id: 1; Molecule: Adenylate 1e4y [ B ] 4ake [ B ] 214

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