2PV7

Crystal structure of chorismate mutase / prephenate dehydrogenase (tyrA) (1574749) from Haemophilus influenzae RD at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb2PV7/pdb

Classification: ISOMERASE, OXIDOREDUCTASE
Organism(s): Haemophilus influenzae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-09 Released: 2007-05-22
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.194
R-Value Work: 0.161
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes.

Chiu, H.J., Abdubek, P., Astakhova, T., Axelrod, H.L., Carlton, D., Clayton, T., Das, D., Deller, M.C., Duan, L., Feuerhelm, J., Grant, J.C., Grzechnik, A., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Krishna, S.S., Kumar, A., Marciano, D., McMullan, D., Miller, M.D., Morse, A.T., Nigoghossian, E., Okach, L., Reyes, R., Tien, H.J., Trame, C.B., van den Bedem, H., Weekes, D., Xu, Q., Hodgson, K.O., Wooley, J., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1317-1325

PubMed: 20944228 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309110021688
Primary Citation of Related Structures:
2PV7

PubMed Abstract:

Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)(+)-dependent oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD(+) has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α-β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP(+) and NAD(+). The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365' (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.

Organizational Affiliation:

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.

Macromolecule Content

Total Structure Weight: 70.24 kDa
Atom Count: 4,983
Modelled Residue Count: 556
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]	A, B	298	Haemophilus influenzae	Mutation(s): 8 Gene Names: 1574749, tyrA, HI1290 EC: 5.4.99.5 (PDB Primary Data), 1.3.1.12 (PDB Primary Data)
UniProt
Find proteins for P43902 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43902 Go to UniProtKB: P43902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43902
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction
TYR Query on TYR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	TYROSINE C₉ H₁₁ N O₃ OUYCCCASQSFEME-QMMMGPOBSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.194
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M32PV7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.79	α = 90
b = 127.79	β = 90
c = 100.62	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing