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Class 1 Asparaginases

Class Overview

72 experimentally studied proteins

74 sequences in Swiss-Prot

64,284 unique sequences in UniRef100

Bacteria, archaea and eukaryotes (animals, fungi, protozoans, algea)

Affinities to l‑asparagine and sometimes l‑glutamine or other substrates

N-terminal catalytic and C-terminal stabilizing domains

Tetrameric or dimeric structures

Reference Monomer1

Reference Structure

Clan 1 Clan 2 Clan 3 Clan 4 Clan 5
Family 1 Mostly fungal asparaginases, contains the Saccharomyces cerevisiae isoenzymes. Family 5 Contains the Bacillus lichenformis asparaginase, a dimeric enzyme with a Km in the lower millimolar range. Family 8 A diverse family with poorly conserved motifs. Family 10 A family of short chain asparaginases that lack the C-terminal stabilizing domain. Family 14 Mostly animal asparaginases / lysophospholipases with additional ankyrin repeats, like the human and guinea pig enzymes.
Family 2 Putative bacterial asparaginases. Family 6 Contains the Mycobacterium tuberculosis asparaginase, a dimeric secretory enzyme. Family 9 Putative bacterial asparaginases. Family 11 Although a family of mostly bacterial asparaginases, it also contains the dimeric archaeal asparagianses from Pyrococcus furiosus and Thermococcus kodakarensis. Family 15 Mostly fungal asparaginases with additional ankyrin repeats. Contains the Rhizomucor miehei asparaginase with a Km in the micromolar range.
Family 3 Contains the classic "type II" asparaginases, like the Escherichia coli and Dickeya chrysanthemi asparaginases in pharmaceutical use. Family 7 Putative bacterial asparaginases with a unique leucine in the conserved Motif 1. Family 12 The Glutamyl-tRNA amido-transferase subunit D family, a group of achaeal enzymes that also contain the Class 1 asparaginase domain. Family 16 Asparaginases mostly from Pseudomonadota, most notably the "type I" Escherichia coli and Yersinia pestis enzymes.
Family 4 Putative bacterial asparaginases. Family 13 Putative bacterial and archaeal asparaginases. Family 17 A diverse family of putative asparaginases from bacteria and eukaryotes, which often contain an additional unidentified domain.
Family 18 Almost exclusively putative asparaginases of bacteria belonging to the Bacteroidota phylum.

Experimentally Studied Proteins

Fam ? Class - Clan - Family Alt ? Alternative historical name / classification AN ? UniProt accession number Name ? UniProt entry name, only given here for Swiss-Prot entries EC Organism Cell-Loc AAs Structure PDB Km i for Asn [mM] Vmax i for Asn [μmol/min/mg] Kcat i for Asn [s-1]

Swiss-Prot Sequences

Fam ? Class - Clan - Family Alt ? Alternative historical name / classification AN ? UniProt accession number Name ? UniProt entry name, only given here for Swiss-Prot entries EC Organism Cell-Loc AAs Structure PDB Km i for Asn [mM] Vmax i for Asn [μmol/min/mg] Kcat i for Asn [s-1]

UniRef100 Sequences2

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Phylogenetic Tree and Introduction

Class 1 l‑asparaginases, previously bacterial-type l‑asparaginases, are the largest and most studied class that contain both l‑asparaginases in pharmaceutical use. Class 1 l‑asparaginases can be found in bacteria, archaea, and eukaryotes, including humans. They display a range of affinities to l‑asparagine, l‑glutamine and sometimes other substrates, such as 1-acyl-sn-glycero-3-phosphocholine or l‑glutamyl-tRNA(Gln), however the l‑asparaginases with the highest affinities to l‑asparagine can be found in this class.

Although sequence similarity can be quite low between sequences, the tertiary structure of the L-asparaginase domain is well conserved throughout the class. This class typically consists of a N-terminal catalytic domain and a C-terminal stabilizing domain connected by a linker, which make up the Class 1 l‑asparaginase monomer. An exception to this are Family 10 l‑asparaginases, which lack the C-terminal stabilizing domain. Family 14 and Family 15 also tend to have additional ankyrin repeats.

Structurally, the l‑asparaginases in this class tend to organize into tetramers and sometimes dimers.

Phylogenetic tree

Representative Sequence Alignment

Conserved Motifs of Families

Motifs Image

Families Overview

Clan Family UniProt ID: (name, PDB) Activity Extra domains Protein structure Molecular weight Taxonomy Cell location Km (Asn)
1 1 S*: P38986
(ScAI)
S*: P0CX78 (ScAII)
ASNase with minimal GLNase signal seq. (most) - ~40 kDa eukaryotes (fungi)
bacteria (some)
secreted
cytoplasm
μM
mM
2 U: A0A931LDC7
U: E3QQI5
ASNase (putative) signal seq. (some) - - bacteria - -
3 S*: P00805
(EcAII, 3ECA)
S*: P06608
(ErAII, 5F52)
ASNase with low GLNase
GLNase with lower ASNase
signal seq. (some) homo tetramer ~35 kDa bacteria periplasm
cytoplasm
μM
mM
4 U: W7NWT6
U: A0A0N7J905
ASNase (putative) signal seq. (few) - - bacteria - -
2 5 S*: P30363
(BlA, 7C8X i Sequence may be not be exact match )
U: U5T4E5
ASNase with minimal GLNase - homo dimer ~37 kDa bacteria - μM
mM
6 S*: P9WPX5 (MtA)
S: Q9RRX9
ASNase - dimer ~36 kDa bacteria secreted mM
7 U: C1B6A9
U: U2BE30
ASNase (putative) - - - bacteria - -
3 8 U: E3CWW1
U: K0KG84
ASNase (putative) disorder. regions (some)
signal seq. (some)
repeats (some)
- - bacteria
eukaryotes (algae, fungi, metazoans)
- -
9 U: A0A6N3EMU0
U: A0A928JPL4
ASNase (putative) - - - bacteria - -
4 10 U*: Q2RMX1
(RrA, 8UOO)
U: G2IJ92
ASNase lack C-terminal ASNase domain homo tetramer ~18 kDa bacteria - mM
11 S*: Q8TZE8
(PfA, 4Q0M)
S*: Q5JIW4
(TkA, 5OT0)
ASNase - homo dimer ~37 kDa bacteria (mostly bacillota)
archaea
cytoplasm μM
mM
12 S*: Q9V0T9 (1ZQ1)
S*: O26802 (2D6F)
glutamyl-tRNA amido-transferase subunit D extra ~100 amino acid domain hetero tetramer ~50 kDa archaea
bacteria (some)
-
13 U: K2BPI2
U: B7G6G9
ASNase (putative) - - - bacteria
archaea (some)
- -
5 14 S*: Q86U10 (HsAI)
U*: H0W0T5
(CpAI, 4R8L)
lysophospholipase, trans-acetylase, acetyl-hydrolase, ASNase ankyrin repeats (most) tetramer (dimer of dimers) ~60 kDa eukaryotes (mostly metazoans) - μM
mM
15 U*: W0G253 (RmAI)
U: D0LXX2
ASNase with minimal GLNase ankyrin repeats (most) homo dimer (putative) ~72 kDa eukaryotes (mostly fungi)
bacteria (some)
- μM
16 S*: P0A962
(EcAI, 2HIM)
U*: A0A3N4B0Q2
(YpAI, 7R69)
ASNase with minimal GLNase - tetramer (dimer of two intimate dimers)
homo dimer
~37 kDa bacteria (mostly pseudo-monadota) cytoplasm mM
17 U: A0A318KGZ9
U: A0A1G7HJG0
ASNase (putative) additional amino acid chain (often)
C-terminal domain (often)
- - bacteria
eukaryotes (sar, algae, fungi, discoba)
- -
18 U: A0A653PC67
U: G8R309
ASNase (putative) - - - bacteria (bacteroidota) - -

Entry: S = Swiss-Prot, U = UniProtKB, P = UniParc, * = experimentally studied protein, UniProt accession number (short protein name, PDB id). Activity: ASNase = l‑asparaginase, GLNase = l‑glutaminase. Molecular weight is for a monomeric unit. Km is for l‑asparagine: μM = Km < 1 mM, mM = Km ≥ 1 mM.


1Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024). Licensed under CC BY 4.0.

2Suzek, B.E. et al. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (2007). Licensed under CC BY 4.0. Added classification code to sequence headers.


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