Phosphoribosylanthranilate isomerase

In enzymology, a phosphoribosylanthranilate isomerase [ PRAI ] (EC

phosphoribosylanthranilate
5.3.1.24 (https://enzyme.expasy.org/EC/5.3.1.24)) is an enzyme that catalyzes
isomerase
the third step of the synthesis of the amino acid tryptophan.[1]

This enzyme participates in the phenylalanine, tyrosine and tryptophan

biosynthesis pathway, also known as the aromatic amino acid biosynthesis
pathway

In yeast it is encoded by the TRP1 gene.[2]

Contents 3D rendering of
Nomenclature Phosophoribosylanthranilate
Reaction[4] Isomerase
Kinetics Identifiers
Structure EC 5.3.1.24 (https://www.qm
Active Site[7] number ul.ac.uk/sbcs/iubmb/enzy
Inhibitors me/EC5/3/1/24.html)
Molecular Weight[3] CAS 37259-82-8 (http://www.c
Homologous genes number ommonchemistry.org/Che
References micalDetail.aspx?ref=372
59-82-8&title=)
Further reading
Databases
IntEnz IntEnz view (https://www.
Nomenclature ebi.ac.uk/intenz/query?c
md=SearchEC&ec=5.3.1.
This enzyme belongs to the family of isomerases, specifically those
24)
intramolecular oxidoreductases interconverting aldoses and ketoses. The
systematic name of this enzyme class is N-(5-phospho-beta-D- BRENDA BRENDA entry (http://ww
ribosyl)anthranilate aldose-ketose-isomerase. Other names in common use w.brenda-enzymes.org/e
include: nzyme.php?ecno=5.3.1.2
4)
PRA isomerase,
ExPASy NiceZyme view (http://ww
PRAI,
IGPS:PRAI (indole-3-glycerol-phosphate, w.expasy.org/enzyme/5.3.
synthetase/N-5'-phosphoribosylanthranilate isomerase complex), 1.24)
and
KEGG KEGG entry (https://www.
N-(5-phospho-beta-D-ribosyl)anthranilate ketol-isomerase.
genome.jp/dbget-bin/ww
xPRAI (monomeric variant in Saccharmyces cerevisiae)[3]
w_bget?enzyme+5.3.1.2
PRAI[ML256-452] (engineered variant of 1-(2-carboxy-
phenylamino)-1-deoxy-D-ribulose 5-phosphate carboxylase: 4)
PRAI)[3] MetaCyc metabolic pathway (http
s://biocyc.org/META/subs
Reaction[4] tring-search?type=NIL&o
bject=5.3.1.24)
Phosphoribosylanthranilate isomerase is one of the many enzymes within the PRIAM profile (http://priam.prabi.f
biosynthesis pathway of tryptophan (an essential amino acid). The upstream* r/cgi-bin/PRIAM_profiles_
pathway substrates and intermediates are shown below (Fig. 2). CurrentRelease.pl?EC=5.
As seen in Fig. 3, N-(5'-phosphoribosyl)-anthranilate via this enzyme is
3.1.24)
converted into 1-(o-carboxyphenylamino)-1-deoxribulose 5-phosphate. As the PDB RCSB PDB (http://www.rcsb.o
name phosphoribosylanthranilate isomerase suggests, it functions as an structures rg/pdb/search/smartSubquery.
isomerase, rearranging the parts of the molecule without adding or removing do?smartSearchSubtype=Enz
molecules or atoms. ymeClassificationQuery&Enzy
me_Classification=5.3.1.24)
The reaction seen in Fig. 3, is an intramolecular redox (reduction-oxidation)
PDBe (https://www.ebi.ac.uk/
reaction.[5] Its first step involves a proton transfer. This product intermediate,
pdbe/entry/search/index?ec_n
an enolamine, is fluorescent, which is useful for kinetic studies
umber:5.3.1.24) PDBsum (htt
within this pathway.[5] However, this product is unstable, and quickly ps://www.ebi.ac.uk/thornton-sr
isomerases into an α-amino keto. v/databases/cgi-bin/enzymes/
GetPage.pl?ec_number=5.3.
1.24)

Gene AmiGO (http://amigo.geneont

Ontology ology.org/amigo/term/GO:000
4640) / QuickGO (https://ww
w.ebi.ac.uk/QuickGO/term/G
O:0004640)

Search

PMC articles (https://www.ncbi.nlm.ni

h.gov/entrez/query.fcgi?db=pub
med&term=5.3.1.24%5BEC/R
N%20Number%5D%20AND%2
0pubmed%20pmc%20local%5B
sb%5D)

PubMed articles (https://www.ncbi.nlm.ni

h.gov/entrez/query.fcgi?db=pub
Fig. 2: Upstream* Pathway of Tryptophan
med&term=5.3.1.24%5BEC/R
Synthesis N%20Number%5D)

NCBI proteins (https://www.ncbi.nlm.n

ih.gov/protein?term=5.3.1.24%5
BEC/RN%20Number%5D)
 Fig 3: Enzyme Isomerase Reaction

Fig. 4: Downstream* Pathway of Tryptophan

Synthesis

Note: Upstream/Downstream are relative to the compounds/molecules directly involved in

phosphoribosylanthranilate isomerase reaction

Kinetics
Michaelis-Menten kinetic data, is given in the table below for PRAI and indole-glycerol-phosphate synthase (IGPS, EC
4.1.1.48).[6]
 Table 1: Kinetic Data
Km kcat
Enzyme Temperature (°C) (μM) (1/sec)

tPRAI 25 0.280 3.7

45 0.390 13.5
60 0.730 38.5
80 1.030 116.8
tIGPS 25 0.006 0.11
45 0.014 0.75
60 0.053 3.24
80 0.123 15.4

Structure
Depending on the microorganism PRAI's structure can vary between a
mono-functional enzyme (monomeric and labile) or a stable bi-functional
dimeric enzyme. Within Saccharomyces cerevisiae, Bacillus subtilis,
Pseudomonas putida, and Acinetobacter calcoaceticus the enzyme is
monmeric.[7] In contrast, in hyperthermophile Thermotoga maritima,
Escherichia coli (Fig. 5), Salmonella typhimurium, and Aerobacter
aerogenes, and Serratia marcescens, it is a bi-functional enzyme with
indoleglycerol phosphate synthase as the paired enzyme.[8]

The crystal structure has been characterized for a variety of the above
Fig 6: Structure of N-(5'-phophoribosyl) listed microorganisms. The known 2.0 A structure of PRAI from
anthranilate isomerase from Pyrococcus Pyrococcus furiosus shows that tPRAI has a TIM-barrel fold (Fig. 6).
furiosus PRAI derived from Thermococcus kodakaraensis also expresses a similar
TIM-barrel fold structure.[7] The subunits of tPRAI associate via the N-
terminal faces of their central beta-barrels. Two long, symmetry-related
loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the
side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster,
and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability
of tPRAI.[9]

The bi-functional version of this enzyme isolated from E. Coli (Fig. 5) performs two steps within the Tryptophan pathway.
Referencing Fig. 7, the N-terminal catalyzes the IGPS reaction (residues ~1-289 purple), and the C-terminal domain performs the
PRAI reaction (residues ~158-452 turquoise). Although these domains overlap (orange), the active sites are not overlapping, and
studies have shown that mono-functional enzymes composing of these two domains are still able to produce a functional
tryptophan bio-synthetic pathway.[10]

The βα loops are responsible for the activity of this enzyme, and the αβ loops are involved in the protein's stability.[8]

More details on the discovery of this enzyme's structure can be found in Willmann's paper.[11]

Active Site[7]
 Specifically, for phosphoribosyl anthranilate isomerase, TkTrpF, from
Thermococcus kodakaraensis. The active site for the Amadori rearrangement,
was determined to be Cys8 (acting as the general base) and Asp135 (as the
general acid).[12]

Inhibitors
An enzyme inhibitor[13] is molecule that binds to an enzyme that therefore
Fig 5: Three dimensional structure of decreases the activity of the protein. The following molecules have been shown
the bi-functional PRAI: IGPS enzyme
to inhibit PRAI acivity:
from E. Coli
Reduced 1-(2-carboxyphenylamino )-1-deoxy-D-ribulose 5-phosphate [5, 6,8);
Indoleglycerol phosphate (8); Indolepropanol phosphate (8); MnCI2 CoCI2 [16);
CuS04 (16); More (chemically synthesized N-(5-phospho-betaD-
ribosyl)anthranilate contains inhibitors, but not if it is generated by anthranilate
phosphoribosyltransferase)

Fig 7: IGPS (purple), shared Molecular Weight[3]

(orange), and PRAI (turquoise)
26300 (Bacillus subtilis, gel filtration)
reaction domains
45000 (Aeromonas formicans, Serratia marinorubra, gel filtration, indole-3-

glycerol-phosphate synthetase/N-5'-phosphoribosylanthranilate isomerase

complex)

46000 (E. coli, sedimentation equilibrium)

47000 (Citrobacter ballerupensis, gel filtration, indole-3-glycerol-phosphate

synthetase/N-5'-phosphoribosylanthranilate isomerase complex)

48000 (Serratia marcescens , Erwinia carotovora , gel filtration , indole-3-glycerol-phosphate synthetase/N-5'-

phosphoribosylanthranilate

isomerase complex )

49370 (E. coli, calculated from gene sequence)

53000 (Proteus vulgaris, gel filtration, indole-3-glycerol-phosphate synthetase/

N-5'-phosphoribosylanthranilate isomerase complex)

160000 (Neurospora crassa, gel filtration, component lib of the anthranilate

synthetase complex has N-(5'-phosphoribosyl)anthranilate isomerase and

indole-3-glycerol phosphate synthetase activities)

185000 (Hansenula henricii, gel filtration, indole-3-glycerol-phosphate synthetase/

N-5'-phosphoribosylanthranilate isomerase complex)

Homologous genes
There are homologous genes which produce this enzyme in plant species such as Arabidopsis thaliana and Oryza sativa (Asian
Rice). One form of bacterium it is found in Thermotoga maritima.

Phosphoribosylanthranilate isomerase is also found in various forms of fungi such as Kluyveromyces lactis (yeast),
Saccharomyces cerevisiae (yeast), and Ashbya gossypii.[14]

A list of genes encoding for PRAI can also be found on KEGG Enzyme database.[15]

References
1. Creighton TE, Yanofsky C (1970). "Chorismate to tryptophan (Escherichia coli) - Anthranilate synthetase, PR
transferase, PRA isomerase, InGP synthetase, tryptophan synthetase". Methods Enzymol. Methods in
Enzymology. 17A: 365–380. doi:10.1016/0076-6879(71)17215-1 (https://doi.org/10.1016%2F0076-6879%2871%
2917215-1). ISBN 9780121818746.
2. "TRP1/YDR007W Summary" (https://www.yeastgenome.org/locus/S000002414). Saccharomyces genome
database. Stanford University.
3. Schomburg, Dietmar; Stephan, Dörte (1994). Enzyme handbook. Springer-Verlag. ISBN 9783642579424.
OCLC 859587801 (https://www.worldcat.org/oclc/859587801).
4. Lubert Stryer (2019-03-25). Biochemistry. ISBN 9781319114657. OCLC 1052398743 (https://www.worldcat.org/o
clc/1052398743).
5. Hommel U, Eberhard M, Kirschner K (April 1995). "Phosphoribosyl anthranilate isomerase catalyzes a reversible
amadori reaction". Biochemistry. 34 (16): 5429–39. doi:10.1021/bi00016a014 (https://doi.org/10.1021%2Fbi0001
6a014). PMID 7727401 (https://www.ncbi.nlm.nih.gov/pubmed/7727401).
6. Sterner R, Merz A, Thoma R, Kirschner K (2001). "Phosphoribosylanthranilate isomerase and indoleglycerol-
phosphate synthase: tryptophan biosynthetic enzymes from Thermotoga maritima". Methods in Enzymology.
331: 270–80. doi:10.1016/S0076-6879(01)31064-9 (https://doi.org/10.1016%2FS0076-6879%2801%2931064-9).
ISBN 9780121822323. PMID 11265469 (https://www.ncbi.nlm.nih.gov/pubmed/11265469).
7. Perveen, S.; Rashid, N.; Papageorgiou, A.C. (2016-11-09). "Phosphoribosyl anthranilate isomerase from
Thermococcus kodakaraensis". doi:10.2210/pdb5lhf/pdb (https://doi.org/10.2210%2Fpdb5lhf%2Fpdb).
8. Thoma R, Hennig M, Sterner R, Kirschner K (March 2000). "Structure and function of mutationally generated
monomers of dimeric phosphoribosylanthranilate isomerase from Thermotoga maritima". Structure. 8 (3): 265–
76. doi:10.1016/s0969-2126(00)00106-4 (https://doi.org/10.1016%2Fs0969-2126%2800%2900106-4).
PMID 10745009 (https://www.ncbi.nlm.nih.gov/pubmed/10745009).
9. Hennig M, Sterner R, Kirschner K, Jansonius JN (May 1997). "Crystal structure at 2.0 A resolution of
phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants
of protein stability". Biochemistry. 36 (20): 6009–16. doi:10.1021/bi962718q (https://doi.org/10.1021%2Fbi962718
q). PMID 9166771 (https://www.ncbi.nlm.nih.gov/pubmed/9166771).
10. Eberhard M, Tsai-Pflugfelder M, Bolewska K, Hommel U, Kirschner K (April 1995). "Indoleglycerol phosphate
synthase-phosphoribosyl anthranilate isomerase: comparison of the bifunctional enzyme from Escherichia coli
with engineered monofunctional domains". Biochemistry. 34 (16): 5419–28. doi:10.1021/bi00016a013 (https://doi.
org/10.1021%2Fbi00016a013). PMID 7727400 (https://www.ncbi.nlm.nih.gov/pubmed/7727400).
11. PDB: 1PII (https://www.rcsb.org/structure/1PII); Wilmanns M, Priestle JP, Niermann T, Jansonius JN (January
1992). "Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase:
indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution". Journal of Molecular Biology.
223 (2): 477–507. doi:10.1016/0022-2836(92)90665-7 (https://doi.org/10.1016%2F0022-2836%2892%2990665-
7). PMID 1738159 (https://www.ncbi.nlm.nih.gov/pubmed/1738159).
12. Pitt, Charles (2002). Sax, Adolphe (opera). Oxford Music Online. Oxford University Press.
doi:10.1093/gmo/9781561592630.article.o006145 (https://doi.org/10.1093%2Fgmo%2F9781561592630.article.o
006145).
13. "Enzyme→ Inhibitor List: M", Handbook of Enzyme Inhibitors (https://archive.org/details/handbookofenzyme00hel
m), Wiley-VCH Verlag GmbH, 1999, pp. 894–956, doi:10.1002/9783527618330.ch13 (https://doi.org/10.1002%2
F9783527618330.ch13), ISBN 9783527618330
14. "Blast search for phosphoribosylanthranilate isomerase" (https://www.ncbi.nlm.nih.gov/homologene/?term=phosp
horibosylanthranilate%20isomerase). HomoloGene Database. National Center for Biotechnology Information.
15. "KEGG Enzyme" (https://www.genome.jp/dbget-bin/www_bget?ec:5.3.1.24).

Further reading
Braus GH, Luger K, Paravicini G, Schmidheini T, Kirschner K, Hütter R (June 1988). "The role of the TRP1 gene
in yeast tryptophan biosynthesis". The Journal of Biological Chemistry. 263 (16): 7868–75. PMID 3286643 (http
s://www.ncbi.nlm.nih.gov/pubmed/3286643).

This article incorporates text from the public domain Pfam and InterPro: IPR001240 (https://www.ebi.a
c.uk/interpro/entry/IPR001240)

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