Role of the N-terminal extension of the (betaalpha)8-barrel enzyme indole-3-glycerol phosphate synthase for its fold, stability, and catalytic activity.


Abstract

Indole-3-glycerol phosphate synthase (IGPS) catalyzes the fifth step in the biosynthesis of tryptophan. It belongs to the large and versatile family of (betaalpha)(8)-barrel enzymes but has an unusual N-terminal extension of about 40 residues. Limited proteolysis with trypsin of IGPS from both Sulfolobus solfataricus (sIGPS) and Thermotoga maritima (tIGPS) removes about 25 N-terminal residues and one of the two extra helices contained therein. To assess the role of the extension, the N-terminally truncated variants sIGPSDelta(1-26) and tIGPSDelta(1-25) were produced recombinantly in Escherichia coli, purified, and characterized in comparison to the wild-type enzymes. Both sIGPSDelta(1-26) and tIGPSDelta(1-25) have unchanged oligomerization states and turnover numbers. In contrast, their Michaelis constants for the substrate 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate are increased, and their resistance toward unfolding induced by heat and guanidinium chloride is decreased. sIGPSDelta(1-26) was crystallized, and its X-ray structure was solved at 2.8 A resolution. The comparison with the known structure of sIGPS reveals small differences that account for its reduced substrate affinity and protein stability. The structure of the core of sIGPSDelta(1-26) is, however, unchanged compared to sIGPS, explaining its retained catalytic activity and consistent with the idea that it evolved from the same ancestor as the phosphoribosyl anthranilate isomerase and the alpha-subunit of tryptophan synthase. These (betaalpha)(8)-barrel enzymes catalyze the reactions preceding and following IGPS in tryptophan biosynthesis but lack an N-terminal extension. Study holds ProTherm entries: 18881, 18882, 18883, 18884 Extra Details: (betaalpha)(8)-barrel enzymes; substrate affinity; protein stability; tryptophan biosynthesis

Submission Details

ID: gq6ZqVy63

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:50 p.m.

Version: 1

Publication Details
Schneider B;Knöchel T;Darimont B;Hennig M;Dietrich S;Babinger K;Kirschner K;Sterner R,Biochemistry (2005) Role of the N-terminal extension of the (betaalpha)8-barrel enzyme indole-3-glycerol phosphate synthase for its fold, stability, and catalytic activity. PMID:16342933
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
5AOU 2016-08-17 1.1 Structure of the engineered retro-aldolase RA95.5-8F apo
4A29 2012-11-07 1.1 Structure of the engineered retro-aldolase RA95.0
5AN7 2016-08-17 1.1 Structure of the engineered retro-aldolase RA95.5-8F with a bound 1,3-diketone inhibitor
4OU1 2014-03-05 1.25 Crystal structure of a computationally designed retro-aldolase covalently bound to folding probe 1 [(6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol]
4A2R 2012-11-07 1.3 Structure of the engineered retro-aldolase RA95.5-5
5K7J 2016-08-03 1.39 Structure of designed zinc binding protein ZE2 bound to Zn2+
4A2S 2012-11-07 1.4 Structure of the engineered retro-aldolase RA95.5
3TC7 2011-08-24 1.5 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR62.
3NYZ 2011-06-29 1.51 Crystal Structure of Kemp Elimination Catalyst 1A53-2
3NZ1 2011-06-29 1.56 Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole
3TC6 2011-08-24 1.6 Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63.
4LNY 2013-08-07 1.93 Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR422
1IGS 1996-07-11 2.0 INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS AT 2.0 A RESOLUTION
1A53 1999-03-23 2.0 COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION
1JUL 1997-07-07 2.0 INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A SECOND ORTHORHOMBIC CRYSTAL FORM
1LBF 2002-06-12 2.05 CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WITH REDUCED 1-(O-CABOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP)
4IWW 2013-08-21 2.3 Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy
1LBL 2002-09-18 2.4 Crystal structure of indole-3-glycerol phosphate synthase (IGPS) in complex with 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (CdRP)
4IX0 2013-08-21 2.5 Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy
1I4N 2002-03-20 2.5 CRYSTAL STRUCTURE OF INDOLEGLYCEROL PHOSPHATE SYNTHASE FROM THERMOTOGA MARITIMA
1JUK 1997-07-07 2.5 INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A TRIGONAL CRYSTAL FORM
2C3Z 2005-10-13 2.8 Crystal structure of a truncated variant of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus
6NW4 2019-07-24 3.0 Evolution of a computationally designed Kemp eliminase
1J5T 2002-07-31 3.0 Crystal structure of indole-3-glycerol phosphate synthase (TM0140) from Thermotoga maritima at 3.0 A resolution

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Indole-3-glycerol phosphate synthase Q56319 TRPC_THEMA
100.0 Indole-3-glycerol phosphate synthase Q06121 TRPC_SACS2
100.0 Multifunctional tryptophan biosynthesis protein P25170 TRPG_PHACH