Protein Modeling Worksheet

Part 1: Examining High Quality Protein Structures

NAMES: Sarah Reagen

DATE: 10-30-17

PROTEIN (include species): TRIOSEPHOSPHATE ISOMERASE

Go to the PDB website: http://www.rcsb.org/pdb/home/home.do

Use the search function to search for your protein.

Number of hits for this protein (do not include species, just search for the name of your
protein): 208

Structure Chosen: TRIOSEPHOSPHATE ISOMERASE-

PHOSPHOGLYCOLOHYDROXAMATE
References complete with PubMed Abstract:
Structure of the triosephosphate isomerase-phosphoglycolohydroxamate
complex: an analogue of the intermediate on the reaction pathway.
Davenport, R.C., Bash, P.A., Seaton, B.A., Karplus, M., Petsko, G.A., Ringe, D.
(1991) Biochemistry 30: 5821-5826
PubMed Abstract:
The glycolytic enzyme triosephosphate isomerase (TIM) catalyzes the interconversion of the three-
carbon sugars dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) at a rate
limited by the diffusion of substrate to the enzyme. We have solved the three-dimensional structure of
TIM complexed with a reactive intermediate analogue, phosphoglycolohydroxamate (PGH), at 1.9-A
resolution and have refined the structure to an R-factor of 18%. Analysis of the refined structure reveals
the geometry of the active-site residues and the interactions they make with the inhibitor and, by
analogy, the substrates. The structure is consistent with an acid-base mechanism in which the
carboxylate of Glu-165 abstracts a proton from carbon while His-95 donates a proton to oxygen to form
an enediol (or enediolate) intermediate. The conformation of the bound substrate stereoelectronically
favors proton transfer from substrate carbon to the syn orbital of Glu-165. The crystal structure suggests
that His-95 is neutral rather than cationic in the ground state and therefore would have to function as an
imidazole acid instead of the usual imidazolium. Lys-12 is oriented so as to polarize the substrate
oxygens by hydrogen bonding and/or electrostatic interaction, providing stabilization for the charged
transition state. Asn-10 may play a similar role.

Are any of the structures mutants? - no

Are any of the structures protein-protein complexes? - no

1
What kinds structures are there (X-ray, NMR, neutron diffraction, cryoEM, etc.)? –
X-ray diffraction

PDB ID: 7TIM

Classification: Intramolecular oxidoreductase
Method: X-RAY diffraction
Resolution: 1.9 A

Number of Chains: 2 Length of Each Chain: A = 74 A B = 83.5 A

Quaternary Structure: PGH
Ligand(s) (use chemical names): Phosphoglycolohydroxamic acid

CATH Classification Class: Alpha-beta barrel

FASTA Sequence: >7TIM:A|PDBID|CHAIN|SEQUENCE

ARTFFVGGNFKLNGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGA
QNAYLKASGAFTGENSVD
QIKDVGAKWVILGHSERRSYFHEDDKFIADKTKFALGQGVGVILCIGETLEEKKAGKTLD
VVERQLNAVLEEVKDWTNVV
VAYEPVWAIGTGLAATPEDAQDIHASIRKFLASKLGDKAASELRILYGGSANGSNAVTFKD
KADVDGFLVGGASLKPEFV
DIINSRN

Are coordinates for the hydrogens present? - no

Are any of the ligands cofactors (you may need to read the abstract, check a
Biochem text, or Google the protein to answer this)? - No

2
Figures created in VMD with explanatory figure legends; note
each group member should contribute a figure with legend
and each figure should be unique (even if it is of the same
structure).

The image shows the alpha helixes (spirals), the beta-sheets (arrows, which are
parallel), and turns (tubes) of the protein. The image also shows the regional residue
types of the protein such as polar (green), basic (blue), acidic (red), and non-polar
(gray).

3
Discussion (should be written as a group, compare and contrast the different
proteins and protein structures):