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3.4.13.9: Xaa-Pro dipeptidase

This is an abbreviated version!
For detailed information about Xaa-Pro dipeptidase, go to the full flat file.

Word Map on EC 3.4.13.9

Reaction

hydrolysis of Xaa-/-Pro dipeptides; also acts on aminoacyl-hydroxyamine analogues. No action on Pro-Pro =

Synonyms

clan MG aminopeptidase P-like metallopeptidase, dipeptidase, proline, DPP8, EC 3.4.3.7, gamma-peptidase, imidodipeptidase, LGAS_0712, M24B peptidase, More, MP50, OPAA, OPAA-2, organophosphate acid anhydrolase, organophosphate anhydrolase/prolidase, organophosphorus acid anhydrolase, PepD, PepE, PepI, PepQ, peptidase D, peptidase-Q, PepX, Pf-peptidase, Pfprol, PH0974, PH1149, Ph1prol, Phprol, PLD, post-proline-cleaving aminopeptidase, prolidase, prolidase homolog 1, prolidase homolog 2, prolidase I, prolidase II, Proline dipeptidase, proline iminopeptidase, proline-specific amino dipeptidase, prolyl dipeptidase, PRS, QPP, quiescent cell proline dipeptidase, serum prolidase, X-Pro dipeptidase, X-prolyl-dipeptidyl aminopeptidase, Xaa-Pro dipeptidase, XPD, XPD43, XPP

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.13 Dipeptidases
                3.4.13.9 Xaa-Pro dipeptidase

Crystallization

Crystallization on EC 3.4.13.9 - Xaa-Pro dipeptidase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme, hanging drop method, mixing of 0.002 ml of protein solution containing 10 mg/ml protein in 1 mM 2-mercaptoethanol, 0.1 mM MnCl2, and 10 mM Tris-HCl, pH 7.2, with 0.002 ml of reservoir solution containing 16% PEG 4000, 20 mM MnCl2, 1 mM 2-mercaptoethanol, 270 mM ammonium acetate, and 60 mM sodium acetate, pH 4.6, at 20°C, 2-4 days, X-ray diffraction structure determination and analysis
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to 1.4 A resolution. XPP forms a dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other
-
0.0025 ml of purified recombinant enzyme, 10 mg/ml, in 50 mM Tris-HCl, pH 8.5, 6.5-7.5% PEG 8000, 0.1 M magnesium acetate, hanging drop vapour diffusion, against 1.0 ml reservoir solution containing 13-15% PEG 8000, 0.2 M magnesium acetate, 50 mM Tris-HCl, pH 8.5, 20°C, 180 days, addition of solid (2S,3R)-3-amino-2-hydroxy-5-methyl-hexanoyl-proline and 15% 2-methyl-2,4-pentanediol for formation and crystallization of enzyme-inhibitor complex, X-ray structure determination and analysis at 2.0 A resolution of crystal form II
10 mg/ml purified recombinant enzyme in 0.25 M MOPS, pH 7.0, hanging drop vapour diffusion method, 0.0025 ml with equal volume of precipitant solution containing PEG 8000 or PEG 4000, best in 0.1 M Tris-HCl, pH 8.5, 0.2 M magnesium acetate, 13-15% PEG 8000, room temperature, after 1 day cyrstals of form I appear, after 6 months crystals of form II appear, X-ray structure determination and analysis at 3.2 A and 1.95 A resolution for Form I and II, respectively, cryoprotection with solution containing 2-methyl-2,4-pentanediol
-
enzyme with bound Zn2+ substituting Co2+
-
native enzyme and in complex with inhibitor (2S,3R)-3-amino-2-hydroxy-5-methylhexanoyl-proline. One homodimer per asymmetric unit. Each subunit has two domains, the C-terminal domain includes the catalytic site centered on a dinuclear metal cluster
structure of the recombinant enzyme determined at 3.4 A resolution
XPD43 is crystallized to 1.83 A resolution using the microbatch-under-oil technique
purified recombinant detagged isozyme XPD43 by microbatch-under-oil technique, mixing of 0.002 ml of 12 mg/ml protein in 20 mM Tris-HCl pH 8.0, 200 mM NaCl, with 0.002 ml of crystallization solution containing 40 mM KH2PO4, 15% glycerol, and 12% PEG 8000, 45 days, 21°C, X-ray diffraction structure determination and analysis by 1.83 A resolution
structures from crystals with no additional metal added, Mn2+ soaked crystals and Zn2+ soaked crystals solved to 1.83 A, 1.85 A, and 1.95 A resolution, respectively