Skip to content
Snippets Groups Projects
Select Git revision
  • master default protected
  • 2.0.5
  • 2.0.4
  • 2.0.3
  • 2.0.2
  • 2.0.1
  • 2.0.0
  • 1.2.4
  • 1.2.2
  • 1.2.1
  • 1.1.0
  • v1.0.9
12 results
Blame Permalink
enzymes.rst 17.88 KiB

Enzyme definitions

All default available enzymes (enzymes_definition.py) are listed bellow.

For each of them, there is the equivalent in RPG grammar.

In the following, nomenclature of Schechter and Berger is used. Amino acids before the cleavage site are designated as P1, P2, P3, etc in the N-terminal direction, and as P1', P2', P3', etc in the C-terminal direction. For example, with cleavage site represented as '|':

...P3-P2-P1-|-P1'-P2'-P3'...

In RPG, this nomenclature is represented as:

...(P3)(P2)(P1)(,)(P1')(P2')(P3')...

Available enzymes

1: :ref:`arg-c` 2: :ref:`asp-n` 3: :ref:`bnps`
4: :ref:`brom` 5: :ref:`casp1` 6: :ref:`casp2`
7: :ref:`casp3` 8: :ref:`casp4` 9: :ref:`casp5`
10: :ref:`casp6` 11: :ref:`casp7` 12: :ref:`casp8`
13: :ref:`casp9` 14: :ref:`casp10` 15: :ref:`chymh`
16: :ref:`chyml` 17: :ref:`clost` 18: :ref:`cnbr`
19: :ref:`enter` 20: :ref:`fxa` 21: :ref:`ficin`
22: :ref:`form` 23: :ref:`gluc` 24: :ref:`glue`
25: :ref:`gran` 26: :ref:`hydro` 27: :ref:`iodo`
28: :ref:`lysc` 29: :ref:`lysn` 30: :ref:`neut`
31: :ref:`ntcb` 32: :ref:`pap` 33: :ref:`peps13`
34: :ref:`peps2` 35: :ref:`prol` 36: :ref:`protk`
37: :ref:`staphI` 38: :ref:`therm` 39: :ref:`throm`
40: :ref:`thromsg` 41: :ref:`tev` 42: :ref:`tryps`

Arg-C

Arg-C proteinase preferentially cleaves after R (P1)

RPG definition:

cleaving rule:

  • (R,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC

Asp-N

Asp-N Sequencing Grade preferentially cleaves before C or D (P1' )

RPG definition:

cleaving rule:

  • (,C or D)

More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/

BNPS-Skatole

BNPS-Skatole preferentially cleaves after W (P1)

RPG definition:

cleaving rule:

  • (W,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS

Bromelain

Bromelain preferentially cleaves after K, A or Y (P1)

RPG definition:

cleaving rule:

  • (K or A or Y,)

More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410479

Caspase 1

Caspase 1 preferentially cleaves after D (P1) preceded by H, A or T in P2 and preceded by F, W, Y or L in P4. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rule:

  • (F or W or Y or L)()(H or A or T)(D,)

exception rule:

  • (F or W or Y or L)()(H or A or T)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1

Caspase 2

Caspase 2 preferentially cleaves after D (P1) preceded by DVA or DEH. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rules:

  • (D)(V)(A)(D,)
  • (D)(E)(H)(D,)

exception rules:

  • (D)(V)(A)(D,)(P or E or D or Q or K or R)
  • (D)(E)(H)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2

Caspase 3

Caspase 3 preferentially cleaves after D (P1) preceded by DMQ or DEV. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rules:

  • (D)(M)(Q)(D,)
  • (D)(E)(V)(D,)

exception rules:

  • (D)(M)(Q)(D,)(P or E or D or Q or K or R)
  • (D)(E)(V)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3

Caspase 4

Caspase 4 preferentially cleaves after D (P1) preceded by LEV or (W/L)EH. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rules:

  • (L)(E)(V)(D,)
  • (W or L)(E)(H)(D,)

exception rules:

  • (L)(E)(V)(D,)(P or E or D or Q or K or R)
  • (W or L)(E)(H)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4

Caspase 5

Caspase 5 preferentially cleaves after D (P1) preceded by (W/L)EH.

RPG definition:

cleaving rule:

  • (W or L)(E)(H)(D,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5

Caspase 6

Caspase 6 preferentially cleaves after D (P1) preceded by VEI or VEH. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rule:

  • (V)(E)(I or H)(D,)

exception rule:

  • (V)(E)(I or H)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6

Caspase 7

Caspase 7 preferentially cleaves after D (P1) preceded by DEV. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rule:

  • (D)(E)(V)(D,)

exception rule:

  • (D)(E)(V)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7

Caspase 8

Caspase 8 preferentially cleaves after D (P1) preceded by (I/L)ET. It will not cleave if D is followed by P, E, D, Q ,K or R in P1'.

RPG definition:

cleaving rule:

  • (I or L)(E)(T)(D,)

exception rule:

  • (I or L)(E)(T)(D,)(P or E or D or Q or K or R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8

Caspase 9

Caspase 9 preferentially cleaves after D (P1) preceded by LEH.

RPG definition:

cleaving rule:

  • (L)(E)(H)(D,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9

Caspase 10

Caspase 10 preferentially cleaves after D (P1) preceded by IEA.

RPG definition:

cleaving rule:

  • (I)(E)(A)(D,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10

Chymotrypsin high specificity

This chymotrypsin preferentially cleaves after F, Y or W (P1) if not followed by P in P1'. It will not cleave after W followed by M in P1'.

RPG definition:

cleaving rule:

  • (F or Y or W,)

exception rules:

  • (F or Y or W,)(P)
  • (W,)(M)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym

Chymotrypsin low specificity

This chymotrypsin preferentially cleaves after F, L, Y, W, M or H (P1) if not followed by P in P1'. It will not cleave after W followed by M in P1'. It will not cleave after M followed by Y in P1'. It will not cleave after H followed by D/M/W in P1'.

RPG definition:

cleaving rule:

  • (F or L or Y or W or M or H,)

exception rules:

  • (F or L or Y or W or M or H,)(P)
  • (W,)(M)
  • (M,)(Y)
  • (H,)(D or M or W)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym

Clostripain

Clostripain (Clostridiopeptidase B) preferentially cleaves after R (P1).

RPG definition:

cleaving rule:

  • (R,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost

CNBr

CNBr preferentially cleaves after M (P1).

RPG definition:

cleaving rule:

  • (M,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr

Enterokinase

Enterokinase preferentially cleaves after K (P1) preceded by D/E in P2, P3, P4 and P5.

RPG definition:

cleaving rule:

  • (D or E)(D or E)(D or E)(D or E)(K,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter

Factor Xa

Factor Xa preferentially cleaves after R (P1) preceded by G in P2, D/E in P3 and A/F/I/L/V/W/G/T in P4.

RPG definition:

cleaving rule:

  • (A or F or I or L or V or W or G or T)(D or E)(G)(R,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa

Ficin

Ficin preferentially cleaves after G, S, E or Y (P1) preceded by A, V, I, L ,F, Y or W in P2.

RPG definition:

cleaving rule:

  • (A or V or I or L or F or Y or W)(G or S or E or Y,)

More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410578

Formic acid

Formic acid preferentially cleaves after D (P1).

RPG definition:

cleaving rule:

  • (D,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH

Glu-C

Glu-C Sequencing Grade preferentially cleaves after D or E (P1).

RPG definition:

cleaving rule:

  • (D or E,)

More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/

Glutamyl endopeptidase

Glutamyl endopeptidase preferentially cleaves after E (P1).

RPG definition:

cleaving rule:

  • (E,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu

Granzyme B

Granzyme B preferentially cleaves after D (P1) preceded by IEP.

RPG definition:

cleaving rule:

  • (I)(E)(P)(D,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB

Hydroxylamine

Hydroxylamine (NH2OH) preferentially cleaves after N (P1) followed by G in P1'.

RPG definition:

cleaving rule:

  • (N,)(G)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro

Iodosobenzoic acid

Iodosobenzoic acid preferentially cleaves after W (P1).

RPG definition:

cleaving rule:

  • (W,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo

Lys-C

LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K (P1).

RPG definition:

cleaving rule:

  • (K,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysC

Lys-N

LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (P1' ).

RPG definition:

cleaving rule:

  • (,K)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysN

Neutrophil elastase

Neutrophil elastase preferentially cleaves after A or V (P1).

RPG definition:

cleaving rule:

  • (A or V,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Elast

NTCB

NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C (P1' ).

RPG definition:

cleaving rule:

  • (,C)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#NTCB

Papain

Papain preferentially cleaves after R or K (P1) preceded by A, V, I, L ,F, Y or W in P2. It will not cleave if followed by V in P1'.

RPG definition:

cleaving rule:

  • (A or V or I or L or F or Y or W)(R or K,)

exception rule:

  • (A or V or I or L or F or Y or W)(R or K,)(V)

More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606

Pepsin pH 1.3

This pepsin preferentially cleaves around F or L (P1 or P1' ). It will not cleave before F or L in P1' followed by P in P2'. It will not cleave before F or L in P1' preceded by R in P1 or P in P2 or H/K/R in P3. It will not cleave after F or L in P1 followed by P in P2'. It will not cleave after F or L in P1 preceded by P in P2 or H/K/R in P3.

RPG definition:

cleaving rule:

  • (,F or L,)

exception rules:

  • (,F or L)(P)
  • (R)(,F or L)
  • (P)()(,F or L)
  • (H or K or R)()()(,F or L)
  • (F or L,)()(P)
  • (P)(F or L,)
  • (H or K or R)()(F or L,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps

Pepsin pH >=2

This pepsin preferentially cleaves around F, L, W or Y (P1 or P1' ). It will not cleave before F, L, W or Y in P1' followed by P in P2'. It will not cleave before F, L, W or Y in P1' preceded by R in P1 or P in P2 or H/K/R in P3. It will not cleave after F, L, W or Y IN P1 followed by P in P2'. It will not cleave after F, L, W or Y in P1 preceded by P in P2 or H/K/R in P3.

RPG definition:

cleaving rule:

  • (,F or L or W or Y,)

exception rules:

  • (,F or L or W or Y)(P)
  • (R)(,F or L or W or Y)
  • (P)()(,F or L or W or Y)
  • (H or K or R)()()(,F or L or W or Y)
  • (F or L or W or Y,)()(P)
  • (P)(F or L or W or Y,)
  • (H or K or R)()(F or L or W or Y,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps

Proline-endopeptidase

Proline-endopeptidase preferentially cleaves after P (P1) preceded by H, K or R in P2 but will not cleaves if followed by P in P1'.

RPG definition:

cleaving rule:

  • (H or K or R)(P,)

exception rule:

  • (H or K or R)(P,)(P)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Pro

Proteinase K

Proteinase K preferentially cleaves after F, W, Y, T, E, A, V, L or I (P1). The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids.

RPG definition:

cleaving rule:

  • (F or W or Y or T or E or A or V or L or I,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ProtK

Staphylococcal peptidase I

Staphylococcal peptidase I preferentially cleaves after E (P1). It will not cleave after E in P1 preceded by E in P2, but cleaves after E in P1 followed by E in P1'.

RPG definition:

cleaving rule:

  • (E,)

exception rule:

  • (E)(E,)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Staph

Thermolysin

Thermolysin preferentially cleaves before A,F,I,L,M or V (P1' ) when not followed by P in P2' nor preceded by D or E in P1.

RPG definition:

cleaving rule:

  • (,A or F or I or L or M or V)

exception rules:

  • (,A or F or I or L or M or V)(P)
  • (D or E)(,A or F or I or L or M or V)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Therm

Thrombin (PeptideCutter)

This thrombin preferentially cleaves after R (P1). Optimum cleavage is when R is preceded and followed by G (P2 and P1' ). Cleavage also occurs when R is preceded by P in P2 and A, F, I, L, V, W, G or T in P3 and P4. It will not cleave after R followed by D/E in P1' or P2'.

It is not strictly coherent with the definition in PeptideCutter, as in this software there are differences between definition, summary and behavior of this enzyme.

RPG definition:

cleaving rules:

  • (G)(R,)(G)
  • (A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)

exception rules:

  • (A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)
  • (A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)()(D or E)

Warning

the following combined exception (A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)(D or E) cannot be used instead, as it will cleave on [...](R,)(D or E).

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Throm https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288055/

Thrombin SG

This thrombin (Sequencing Grade) preferentially cleaves after R (P1) preceded by P in P2, V in P3 and L in P4 and followed by G in P1' and S in P2'.

This thrombin is defined in several kits (see below).

RPG definition:

cleaving rule:

  • (L)(V)(P)(R,)(G)(S)

More information: see thrombin cleavage kits of Abcam, BioVision, Merck or Novagen.

Tobacco etch virus protease

Tobacco etch virus protease (TEV) preferentially cleaves after Q (P1) when followed by G or S in P1' and preceded by Y in P3 and E in P6.

RPG definition:

cleaving rule:

  • (E)()()(Y)()(Q,)(G or S)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#TEV

Trypsin

Trypsin preferentially cleaves after K or R (P1). It will not cleave after K followed by P in P1' except if W in P2. It will not cleave after R followed by P in P1' except if M in P2. It will not cleave CKD, DKD, CKH, CKY, CRK, RRH nor RRR.

RPG definition:

cleaving rules:

  • (K or R,)
  • (W)(K,)(P)
  • (M)(R,)(P)

exception rules:

  • (K or R,)(P)
  • (C)(K,)(D)
  • (D)(K,)(D)
  • (C)(K,)(H)
  • (C)(K,)(Y)
  • (C)(R,)(K)
  • (R)(R,)(H)
  • (R)(R,)(R)

More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Tryps