Alpha-lytic Protease PDB Codes

α-Lytic Protease

PDB code revision reference resolution description download PDB
3URC 23 May 2012 Kelch, et al 1.10Å T181G mutant of alpha-Lytic Protease 3URC
3URD 23 May 2012 Kelch, et al 1.08Å T181A mutant of alpha-Lytic Protease 3URD
3URE 23 May 2012 Kelch, et al 1.49Å Repack mutant (T181I, W199L, Q210I) of alpha-Lytic Protease 3URE
3M7T 09 Feb 2011 Erciyas, et al (unpub) 1.55Å Crystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant 3M7T
3M7U 09 Feb 2011 Erciyas, et al (unpub) 1.05Å Crystal Structure of Alpha-Lytic Protease SB1+2 R64A/E182Q Mutant 3M7U
2PFE 03 Jul 2007 Kelch, et al. 1.44Å Crystal Structure of Thermobifida fusca Protease A (TFPA) 2PFE
2OUA 09 Feb 2007 Kelch, et al. 1.85Å Crystal Structure of Nocardiopsis Protease (NAPase) 2OUA
2H5C 19 Jul 2006 Fuhrmann, et al. 0.82Å  0.82A resolution crystal structure of alpha-lytic protease at pH 5   2H5C
 1SSX  24 Mar 2004 Fuhrmann, et al. 0.83Å 0.83Å resolution crystal structure of alpha-lytic protease at pH 8 1SSX
    NMR-Davis   WT, Me-O-Suc-Ala-Ala-Pro-Val Boronic acid  
 1QQ4  16 Jun 1999 Derman 1.2Å RH138, GS183, at pH 5.14 1QQ4
 1QRW  16 Jun 1999 Derman 1.2Å RH138, GS183 at pH 8 1QRW
 1QRX  16 Jun 1999 Derman 1.6Å aLP (WT) at pH 5.14 1QRX
    Shortle(Raxis 4) 1.45 Å MA190  
    Shortle   MA190, GV216  
    Shortle   WT, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid  
    Shortle(SSRL) 1.41Å WT, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid  
    Shortle(SSRL) 1.87Å MA190, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid  
    Silverstein 1.6Å MA190 low temperature  
4PRO 1 Oct 1998 Sauter 2.4Å MA213 + WT Pro 4PRO
3PRO 26 Aug 1998 Sauter 1.8Å MA213 + Pro —3 3PRO
2PRO 20 Aug 1998 Sauter 3.0Å Wild type Pro region 2PRO
1BOQ 5 Aug 1998 Peters 2.1Å VI167 1BOQ
1TAL 1 Apr 1997 Rader 1.5Å WT low temperature single model 1TAL
2ULL 26 Nov 1996 Rader 1.5Å WT low temperature multiple models 2ULL
1GBA 29 Jan 1996 Mace 2.15Å MA190, GA216 1GBA
1GBB 29 Jan 1996 Mace 2.15Å MA190, GA216, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid 1GBB
1GBC 29 Jan 1996 Mace 2.2Å MA190, GA216, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid 1GBC
1GBD 29 Jan 1996 Mace 2.2Å MA190, GA216, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid 1GBD
1GBE 29 Jan 1996 Mace 2.3Å MA190, GL216 1GBE
1GBF 29 Jan 1996 Mace 2.15Å MA190, GL216, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid 1GBF
1GBH 29 Jan 1996 Mace 2.2Å MA190, GL216, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid 1GBH
1GBI 29 Jan 1996 Mace 2.3Å MA190, GL216, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid 1GBI
1GBJ 29 Jan 1996 Mace 2.0Å MA190 1GBJ
1GBK 29 Jan 1996 Mace 2.13Å MA190, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid 1GBK
1GBL 29 Jan 1996 Mace 2.15Å MA190, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid 1GBL
1GBM 29 Jan 1996 Mace 2.28Å MA190, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid 1GBM
    Reidhaar-Olson, unpublished   NV217  
    Bone, unpublished   VA218  
[1LPR]*   Bone et al, 1991b 2.12Å MA190, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid  
2LPR 15 Jan 1993 Bone et al, 1991b 2.25Å MA190, Me-O-Suc-Ala-Ala-Pro-Val Boronic acid 2LPR
3LPR 15 Jan 1993 Bone et al, 1991b 2.15Å MA190, Me-O-Suc-Ala-Ala-Pro-Norleu Boronic acid 3LPR
[4LPR]*   Bone et al, 1991b 2.1Å MA190, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid  
5LPR 15 Jan 1993 Bone et al, 1991b 2.13Å MA213, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid 5LPR
6LPR 15 Jan 1993 Bone et al, 1991b 2.10Å MA213, Me-O-Suc-Ala-Ala-Pro-Norleu Boronic acid 6LPR
7LPR 15 Jan 1993 Bone et al, 1991b 2.05Å MA213, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid 7LPR
8LPR 15 Jan 1993 Bone et al, 1991b 2.25Å MA213, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid 8LPR
9LPR 15 Jan 1993 Bone et al, 1991b 2.2Å WT, Me-O-Suc-Ala-Ala-Pro-Leu Boronic acid 9LPR
1P11 15 Jan 1993 Bone et al, 1991a 1.93Å WT complex with phosphonate 1P11
1P12 15 Jan 1993 Bone et al, 1991a 1.9Å WT complex with phosphonate 1P12
1P02 15 Apr 1990 Bone et al, 1989 Biochem 2.0Å WT, Me-O-Suc-Ala-Ala-Pro-Ala Boronic acid 1P02
1P03 15 Apr 1990 Bone et al, 1989 Biochem 2.15Å WT, Me-O-Suc-Ala-Ala-Pro-Val Boronic acid 1P03
1P04 15 Apr 1990 Bone et al, 1989 Biochem 2.55Å WT, Me-O-Suc-Ala-Ala-Pro-Ile Boronic acid 1P04
1P05 15 Apr 1990 Bone et al, 1989 Biochem 2.1Å WT, Me-O-Suc-Ala-Ala-Pro-Norleu Boronic acid 1P05
1P06 15 Apr 1990 Bone et al, 1989 Biochem 2.34Å WT, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid 1P06
1P09 15 Apr 1990 Bone et al, 1989 Nature 2.2Å MA213 1P09
1P10 15 Apr 1990 Bone et al, 1989 Nature 2.25Å MA213, Me-O-Suc-Ala-Ala-Pro-Val Boronic acid 1P10
[1P08]*   Bone et al, 1989 Nature 2.25Å MA190, Me-O-Suc-Ala-Ala-Pro-Phe Boronic acid  
[1P07]*   Bone et al, 1989 Nature 2.15Å MA190  
1P01 15 Apr 1990 Bone et al, 1987 Biochem 2.0Å WT, Boc-Ala-Pro-Val Boronic acid 1P01
2ALP 15 Oct 1989 Fujinaga et al, 1985 1.7Å WT 2ALP

*bracketed id codes are no longer available from the PDB.

References

Bone, R, Shenvi, AB, Kettner, CA, Agard, DA (1987) Serine Protease Mechanism: Structure of an Inhibitory Complex of a-Lytic Protease and a Tightly Bound Peptide Boronic Acid. Biochemistry 26: 7609.

Bone, R, Silen, JL, Agard, DA (1989) Structural Plasticity Broadens the Specificity of an Engineered Protease. Nature 339: 191.

Bone, R, Frank, D, Kettner, CA, Agard, DA (1989) Structural Analysis of Specificity: a-Lytic Protease Complexes with Analogues of Reaction Intermediates. Biochemistry 28: 7600.

Bone, R, Sampson, NS, Bartlett, PA, Agard, DA (1991a) Crystal Structures of a-Lytic Protease Complexes with Irreversibly Bound Phosphonate Esters. Biochemistry 30: 2263.

Bone, R, Fujishige, A, Kettner, CA, Agard, DA (1991b) Structural Basis for Broad Specificity in a-Lytic Protease Mutants. Biochemistry 30: 10388.

Fuhrmann, CN, Brian A. Kelch, Nobuyuki Ota and David A. Agard, The 0.83 Å Resolution Crystal Structure of a-Lytic Protease Reveals the Detailed Structure of the Active Site and Identifies a Source of Conformational Strain. Journal of Molecular Biology, (2004), 338(5), 999-101 (pdf)

Fuhrmann, C.N., Daugherty, M.D., and Agard, D.A., "Subangstrom Crystallography Reveals that Short Ionic Hydrogen Bonds, and Not a His-Asp Low-Barrier Hydrogen Bond, Stabilize the Transition State in Serine Protease Catalysis," JACS, 2006, 128(28), 9086-102 (pdf)

Fujinaga, M, Delbaere, LTJ, Brayer, GD, James, MNG (1985) Refined Structure of a-Lytic Protease 1.7Å resolution: Analysis of Hydrogen Bonding and Solvent Structure. J Mol Biol 131: 479.

Kelch, BA and Agard, DA, "Mesophile versus Thermophile: Insights Into the Structural Mechanisms of Kinetic Stability," J. Mol. Biol., 2007, 370(4), 784-95 (pdf)

Kelch, BA, Eagen, KP, Erciyas, FP, Humphris, EL, Thomason, AR, Mitsuiki, S and Agard, DA, "Structural and Mechanistic Exploration of Acid Resistance: Kinetic Stability Facilitates Evolution of Extremophilic Behavior," Journal of Molecular Biology, (2007), 368(3), 870-883 (pdf)

Kelch BA, Salimi NL, Agard DA., "Functional modulation of a protein folding landscape via side-chain distortion." Proc Natl Acad Sci U S A. (2012), 109(24), 9414-9.(pdf)

Mace, JE, Agard, DA (1995) Kinetic and Structural Characterization of Mutations of Glycine 216 in a-Lytic Protease: A New Target for Engineering Substrate Specificity. J Mol Biol 254: 720.

Rader, SD, Agard, DA (1997) Conformational Substates in Enzyme Mechanism: The 120K Structure of a-Lytic Protease at 1.5Å Resolution. Protein Science 6: 1375.

Peters, RJ et al (1998) Pro Region C-terminus: Protease Active Site Interactions Are Critical in Catalyzing the Folding of a-Lytic Protease. Biochemistry 37: 12058.

Sauter, NK, Mau, T, Rader, SD, Agard, DA (1998) Structure of a-Lytic Protease Complexed with its Pro Region. Nature Structural Biology 5: 945.