Table 5.

Crystal structures of hyperthermophilic proteins and potential stabilizing features

Enzyme (resolution)Stabilizing featuresReference
T. maritima holo-GAPDH (2.5 Å)Additional intramolecular, surface IPsa 192
T. maritima ferredoxin (1.75Å)More charged-neutral H bonds that stabilize the structure of turns or fix turns together; conformational strain release: left-handed helical residues substituted with Gly; strong docking of the protein N terminus 226
T. maritima PGK (2.0 Å)Dipole stabilization of the C and N caps of helices; extension of helix α6 by 4 more residues; more IPs, including 2 IPs that link the enzyme C and N termini together 15
T. maritima phosphorybosyl anthranilate isomerase (2.0 Å)More prolines in loops or at the N terminus of helices; loop α2β3 is highly hydrophobic, completely buried into the interior of another subunit; each subunit's N and C termini form a hydrophobic cluster included in the intersubunit surface 131
T. maritima GDH (3.0 Å)More intrasubunit IPs; smaller intrasubunit cavities; hydrophobic intersubunit interfaces (different from the P. furiosus enzyme) 183
T. maritima lactate dehydrogenase (2.1 Å)More intrasubunit IPs; fewer exposed hydrophobic residues/more Glu and Arg on the surface; higher secondary structure (α and β) content; one more helix on the surface shortens a flexible loop; tighter, hydrophobic, intersubunit contacts 16
T. maritima triosephosphate isomerase (2.85 Å)Increased buried hydrophobic surface; more IPs; protein fusion with PGK 227
T. maritima dihydrofolate reductase (2.1Å)Dimerization involves intersubunit H bonds participating in forming two intermolecular antiparallel β-sheets and tight dimer interface packing 75
A. pyrophilus Fe-superoxide dismutase (1.9 Å)Docking of loop 2 and C terminus in intersubunit contacts; large number of IPs (0.1/residue, not involved in networks) 220
P. furiosus aldehyde ferredoxin oxidoreductase (2.3Å)Reduced surface area/volume ratio (increased packing); more IPs 59
P. furiosus citrate synthase (1.9Å)Increased packing (loop shortening, more buried atoms, no cavities, more intimate intersubunit interactions); more intersubunit IPs; fewer thermolabile residues (Met);loop docking by more IPs 284
P. furiosus GDH (2.2Å)More IPs and IP networks (on the surface and at the intersubunit interfaces) 368
P. furiosusmethionine aminopeptidase (1.75 Å)More IPs and IP networks; more charged-neutral H bonds in α and β structures; same number of buried waters, but the buried waters cross-link areas that are distant in the sequence; stabilization of 2 antiparallel β-strands by prolines; shortening of N and C termini and loop stabilization 327
P. kodakaraensis O 6 methylguanine-DNA methyltransferase (1.8Å)Less hydrophobic, less polar, and more charged enzyme surface; more aromatic residues and aromatic clusters; more intra- and interhelix IPs 127
T. litoralis pyrrolidone carboxyl peptidase (1.73 Å)Intersubunit disulfide bridge; hydrophobic intersubunit interface 310
T. gorgonarius DNA polymerase type B (2.5 Å)Two disulfide bridges; enhanced electrostatic complementarity at the protein-DNA interface; better packing of surface loops 143
M. fervidus histone B (NMR)Less unfavorable surface ionic interactions; filling of a hydrophobic cavity 375
M. kandleri methenyl:tetrahydromethanopterin cyclohydrolase (2.0 Å)Trimer instead of dimer; Increase in hydrophobic intersubunit interactions; docking of loops and N and C termini by intersubunit contacts; decreased hydrophobic surface area and more surface acidic residues prevent enzyme aggregation at high salt concentration 120
M. kandleriformylmethanofuran: tetrahydromethanopterin formyltransferase (1.73Å)Uses the high intracellular salt concentration as stabilizing mechanism; enhanced surface ion pairing probably involving inorganic solvated cations; salting-out effect strengthens the intersubunit hydrophobic interactions; docking of loops and of C and N termini 96
S. solfataricus adenylate kinase (2.6 Å)Strong and rigid central trimer interface, strengthened by a laterally extended β-sheet; trimer rather than monomer 356
S. solfataricus GAPDH (2.05Å)One large IP network (15 residues) at a subunit interface (conserved in other thermophilic archaeal GAPDHs, but not entirely conserved in mesophilic archaeal GAPDHs); one interdomain disulfide bridge 160
S. solfataricus β-glycosidase (2.6 Å)More IP networks; docking of the C terminus on the protein surface; buried water molecules involved in H-bond networks (Hypothesis: the internal solvent clusters and surface IP networks absorb the energy of molecular collisions and damp molecular vibrations, thus increasing the kinetic barrier to unfolding) 5
S. solfataricusindole-3-glycerol phosphate synthase (2.0 Å)Docking of the N terminus by H bonds and IPs; more IPs (24 against 11) that clamp secondary structures together, helix dipole stabilization with Asp or Glu; conformational strain release: helix C capping with Gly; ionic strength has little effect on the number and specificity of intramolecular IPs 130, 185
S. solfataricusFe superoxide dismutase (2.3 Å)No clear reason for stability (far fewer IPs than in the A. pyrophilusenzyme) 345
Sulfolobus strain 7 ferredoxin (2.0 Å)Zinc atom holds the core fold and the N-terminal extension together 107
T. aggregansβ-glycosidase (2.4 Å)More intersubunit IPs (including buried IPs); more buried waters, involved in H-bond networks; enzyme is a tetramer 63
  • a IP, ion pair.