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Literature summary extracted from

  • Are, V.N.; Kumar, A.; Kumar, S.; Goyal, V.D.; Ghosh, B.; Bhatnagar, D.; Jamdar, S.N.; Makde, R.D.
    Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases (2017), Biochim. Biophys. Acta, 1865, 153-164 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.4.13.9 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 Xanthomonas campestris pv. campestris

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.4.13.9 His-Pro substrate inhibition Xanthomonas campestris pv. campestris
3.4.13.9 Leu-Pro substrate inhibition Xanthomonas campestris pv. campestris
3.4.13.9 Lys-Pro substrate inhibition Xanthomonas campestris pv. campestris
3.4.13.9 Pro-Pro substrate inhibition Xanthomonas campestris pv. campestris
3.4.13.9 Tyr-Pro substrate inhibition Xanthomonas campestris pv. campestris
3.4.13.9 Zn2+ inhibitory above 0.01 mM Xanthomonas campestris pv. campestris

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.4.13.9 0.4
-
 Pro-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 0.9
-
 His-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 1.2
-
 Leu-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 1.9
-
 Val-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 2.1
-
 Lys-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3.1
-
 Met-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3.3
-
 Phe-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3.4
-
 Gly-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 5.9
-
 Arg-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 6.6
-
 Leu-Pro pH 7.5, 55°C Mycobacterium tuberculosis
3.4.13.9 7
-
 Tyr-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.4.13.9 Mn2+ maximum activity in presence of Mn2+ ions, addition of 1 mM to the assay Xanthomonas campestris pv. campestris
3.4.13.9 Mn2+ maximum activity in presence of Mn2+ ions, addition of 1 mM to the assay Mycobacterium tuberculosis

Organism

EC Number Organism UniProt Comment Textmining
3.4.13.9 Mycobacterium tuberculosis P9WHS7
-
-
3.4.13.9 Mycobacterium tuberculosis ATCC 25618 P9WHS7
-
-
3.4.13.9 Xanthomonas campestris pv. campestris Q8P839
-
-
3.4.13.9 Xanthomonas campestris pv. campestris DSM 3586 Q8P839
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.4.13.9 Arg-Pro + H2O
-
 Xanthomonas campestris pv. campestris Arg + Pro
-
 ?
3.4.13.9 Arg-Pro + H2O
-
 Xanthomonas campestris pv. campestris DSM 3586 Arg + Pro
-
 ?
3.4.13.9 Gly-Pro + H2O
-
 Xanthomonas campestris pv. campestris Gly + Pro
-
 ?
3.4.13.9 His-Pro + H2O
-
 Xanthomonas campestris pv. campestris His + Pro
-
 ?
3.4.13.9 Leu-Pro + H2O
-
 Xanthomonas campestris pv. campestris Leu + Pro
-
 ?
3.4.13.9 Leu-Pro + H2O best substrate Mycobacterium tuberculosis Leu + Pro
-
 ?
3.4.13.9 Leu-Pro + H2O best substrate Mycobacterium tuberculosis ATCC 25618 Leu + Pro
-
 ?
3.4.13.9 Leu-Pro + H2O
-
 Xanthomonas campestris pv. campestris DSM 3586 Leu + Pro
-
 ?
3.4.13.9 Lys-Pro + H2O
-
 Xanthomonas campestris pv. campestris Lys + Pro
-
 ?
3.4.13.9 Met-Pro + H2O
-
 Xanthomonas campestris pv. campestris Met + Pro
-
 ?
3.4.13.9 Met-Pro + H2O
-
 Mycobacterium tuberculosis Met + Pro
-
 ?
3.4.13.9 Met-Pro + H2O
-
 Mycobacterium tuberculosis ATCC 25618 Met + Pro
-
 ?
3.4.13.9 Met-Pro + H2O
-
 Xanthomonas campestris pv. campestris DSM 3586 Met + Pro
-
 ?
3.4.13.9 additional information decreasing order of preference for the N-terminal residue of the Xaa-Pro dipeptides in presence of Mn2+ ions is Leu, Pro, Phe, Met, Arg, Lys, Ile, Ser, His, Ala, Gly, Val, Asp while in that of Zn2+ ions is Leu, Phe, Met, Pro, Arg, Lys, Ala, Ile, Ser, Gly, Val, Asp Mycobacterium tuberculosis ?
-
 ?
3.4.13.9 additional information enzyme exhibits allosteric behavior and substrate inhibition toward dipeptides Leu-Pro, Pro-Pro, His-Pro, Lys-Pro and Tyr-Pro. The order of preference for the N-terminal residue of the Xaa-Pro dipeptides is similar in presence of Mn2+ ions (in decreasing order: Phe, Ser, Met, Leu, Ala, Pro, His, Arg, Ile, Gly, Val, Asp) and Zn2+ ions (0.005 mM) (Met, Phe, SerN, Leu, Ala, Pro, Arg, Lys, Ile=Gly, Val, Asp). The activity towards all the substrates is 4-5 times higher in presence of Mn2+ than Zn2+ ions Xanthomonas campestris pv. campestris ?
-
 ?
3.4.13.9 additional information decreasing order of preference for the N-terminal residue of the Xaa-Pro dipeptides in presence of Mn2+ ions is Leu, Pro, Phe, Met, Arg, Lys, Ile, Ser, His, Ala, Gly, Val, Asp while in that of Zn2+ ions is Leu, Phe, Met, Pro, Arg, Lys, Ala, Ile, Ser, Gly, Val, Asp Mycobacterium tuberculosis ATCC 25618 ?
-
 ?
3.4.13.9 additional information enzyme exhibits allosteric behavior and substrate inhibition toward dipeptides Leu-Pro, Pro-Pro, His-Pro, Lys-Pro and Tyr-Pro. The order of preference for the N-terminal residue of the Xaa-Pro dipeptides is similar in presence of Mn2+ ions (in decreasing order: Phe, Ser, Met, Leu, Ala, Pro, His, Arg, Ile, Gly, Val, Asp) and Zn2+ ions (0.005 mM) (Met, Phe, SerN, Leu, Ala, Pro, Arg, Lys, Ile=Gly, Val, Asp). The activity towards all the substrates is 4-5 times higher in presence of Mn2+ than Zn2+ ions Xanthomonas campestris pv. campestris DSM 3586 ?
-
 ?
3.4.13.9 Phe-Pro + H2O
-
 Xanthomonas campestris pv. campestris Phe + Pro
-
 ?
3.4.13.9 Phe-Pro + H2O
-
 Mycobacterium tuberculosis Phe + Pro
-
 ?
3.4.13.9 Phe-Pro + H2O
-
 Mycobacterium tuberculosis ATCC 25618 Phe + Pro
-
 ?
3.4.13.9 Phe-Pro + H2O
-
 Xanthomonas campestris pv. campestris DSM 3586 Phe + Pro
-
 ?
3.4.13.9 Pro-Pro + H2O
-
 Xanthomonas campestris pv. campestris Pro + Pro
-
 ?
3.4.13.9 Ser-Pro + H2O
-
 Xanthomonas campestris pv. campestris Ser + Pro
-
 ?
3.4.13.9 Ser-Pro + H2O
-
 Mycobacterium tuberculosis Ser + Pro
-
 ?
3.4.13.9 Ser-Pro + H2O
-
 Mycobacterium tuberculosis ATCC 25618 Ser + Pro
-
 ?
3.4.13.9 Tyr-Pro + H2O
-
 Xanthomonas campestris pv. campestris Tyr + Pro
-
 ?
3.4.13.9 Tyr-Pro + H2O
-
 Mycobacterium tuberculosis Tyr + Pro
-
 ?
3.4.13.9 Val-Pro + H2O
-
 Xanthomonas campestris pv. campestris Val + Pro
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.4.13.9 PepE
-
 Mycobacterium tuberculosis
3.4.13.9 PepQ
-
 Xanthomonas campestris pv. campestris
3.4.13.9 prolidase
-
 Xanthomonas campestris pv. campestris
3.4.13.9 XPD
-
 Xanthomonas campestris pv. campestris

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.4.13.9 55
-
-
 Mycobacterium tuberculosis

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
3.4.13.9 50
-
 100% loss of activity at 50°C in absence of Mn2+ Mycobacterium tuberculosis
3.4.13.9 50
-
 35% loss of activity at 50°C in absence of Mn2+ Xanthomonas campestris pv. campestris
3.4.13.9 65
-
 100% activity up to 65°C in presence of Mn2+ Xanthomonas campestris pv. campestris
3.4.13.9 65
-
 50% loss of activity at 65°C in presence of Mn2+ Mycobacterium tuberculosis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.4.13.9 1000
-
 Leu-Pro pH 7.5, 55°C Mycobacterium tuberculosis
3.4.13.9 3000
-
 Val-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3000
-
 His-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 4500
-
 Pro-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 5000
-
 Leu-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 5700
-
 Lys-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 6100
-
 Gly-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 9100
-
 Met-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 12500
-
 Tyr-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 16900
-
 Phe-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 19800
-
 Arg-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.4.13.9 200
-
 Leu-Pro pH 7.5, 55°C Mycobacterium tuberculosis
3.4.13.9 1600
-
 Val-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 1800
-
 Gly-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 1800
-
 Tyr-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 2700
-
 Lys-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 2900
-
 Met-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3300
-
 Arg-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 3300
-
 His-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 4200
-
 Leu-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 5100
-
 Phe-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris
3.4.13.9 11200
-
 Pro-Pro pH 7.5, 55°C Xanthomonas campestris pv. campestris