PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Deciphering Microbial DUFs
November 2014
Microbiome: Fiber Degraders Revealed
November 2014
New NTF2-like Domains
May 2014
Novel Proteins and Networks: Polysaccharide Metabolism in the Human Gut
May 2014
Discovering Deaminases
January 2014
Bacteria and Bile Salts
September 2013
Exploring the Secretome of Gut Bacteria
September 2011
Ribose production on demand
September 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
A glimpse of NDRG2
April 2011
Sugar switch
December 2010
Isoxanthopterin Deaminase
November 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
First bacterial PH domain
January 2010
Unusual cell division
October 2009
CBS Domain Protein TA0289
February 2009
Imidazolonepropionase (HutI)
December 2008
Aspartate Dehydrogenase
August 2008

Research Themes Novel Proteins

Imidazolonepropionase (HutI)

PSI-SGKB [doi:10.3942/psi_sgkb/fm_2008_12]
Featured System - December 2008
Short description: Histidine is an essential amino acid with several interesting chemical properties.

Histidine is an essential amino acid with several interesting chemical properties. The imidazole ring of histidine can adopt several different charge states at typical cellular conditions, and it interacts strongly with metal ions. All of these properties are demonstrated in the enzyme imidazolonepropionase. This enzyme is one of the community-nominated targets studied by the New York SGX Research Center for Structural Genomics (NYSGXRC) as part of a larger study of enolase and amidohydrolase structural genomics. It performs the third step in the major pathway of histidine degradation, when a water molecule is used to open the histidine ring. Ironically, the active site relies on a constellation of histidine amino acids to perform the histidine-breaking reaction.

Metagenomics Target

This enzyme is found in all kingdoms of life. The NYSGXRC has studied the enzyme in two different organisms. The structure shown at the top (PDB entry 2q09) was obtained from an unknown bacterium found in Craig Venter's Global Ocean Sampling project. This metagenomics study randomly isolates DNA from an entire environmental sample, building up a picture of all of the organisms in the environment. The enzyme shown here was reconstructed based on the genomic information from a random sample taken from the fertile waters of the Sargasso Sea. The NYSGXRC has also studied the form of the enzyme made by the bacterium Agrobacterium tumefaciens, shown in the Jmol image below (PDB entry 2puz).

HutI in Action

The NYSGXRC has studied this enzyme at both the beginning and the end of its reaction. The enzyme from the Sargasso Sea bacterium was solved with an analogue of the substrate, and the similar Agrobacterium enzyme was solved with the product of the reaction. The structures reveal the atomic details of the active site and have revealed many aspects of the reaction mechanism. The active site is centered around an iron ion which is coordinated by a collection of histidine and acidic amino acids. Two additional histidine amino acids and a glutamine perform the hydrogen-shuttling operations in the hydrolysis reaction. Both of these complexes are shown close up in the Jmol images below.

The JSmol tab below displays an interactive JSmol.

Aquaglyceroporin (PDB entry 3c02)

One subunit of aquaglyceroporin is shown here. Glycerol molecules (white and pink spheres) and water (turquoise spheres) are lined up single-file through the channel. Two glycerol molecules are bound at the entrance, waiting to enter, and three are bound within the narrow channel. The narrowest portion of the channel is surrounded by an arginine and two aromatic amino acids (shown here in green), that together form the selectivity filter. In this structure, a glycerol molecule is bound inside th


  1. Tyagi R, Eswaramoorthy S, Burley SK, Raushel FM, Swaminathan S. (2008) A common catalytic mechanism for proteins of the HutI family. Biochemistry 47, 5608-5615.

  2. Tyagi R, Kumaran D, Burley SK, Swaminathan S. (2007) X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 Å resolution. Proteins 15, 652-658.

  3. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. (2004) Environmental genome shotgun sequences of the Sargasso Sea. Science 304, 66-70.

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health