6HQV

Pentafunctional AROM Complex from Chaetomium thermophilum

PDB DOI: https://doi.org/10.2210/pdb6HQV/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-25 Released: 2020-05-06
Deposition Author(s): Arora Verasto, H., Hartmann, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.233
R-Value Work: 0.209
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Architecture and functional dynamics of the pentafunctional AROM complex.

Arora Veraszto, H., Logotheti, M., Albrecht, R., Leitner, A., Zhu, H., Hartmann, M.D.

(2020) Nat Chem Biol 16: 973-978

PubMed: 32632294 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41589-020-0587-9
Primary Citation of Related Structures:
6HQV

PubMed Abstract:
The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.

Organizational Affiliation

Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 352.94 kDa
Atom Count: 23,618
Modelled Residue Count: 3,091
Deposited Residue Count: 3,178
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentafunctional AROM polypeptide	A, B	1,589	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0008860 EC: 4.2.1.10 (PDB Primary Data), 2.7.1.71 (PDB Primary Data), 4.2.3.4 (PDB Primary Data), 2.5.1.19 (PDB Primary Data), 1.1.1.25 (PDB Primary Data)
UniProt
Find proteins for G0S061 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S061 Go to UniProtKB: G0S061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S061
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
SKM (Subject of Investigation/LOI) Query on SKM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	H [auth A] I [auth A] K [auth A] R [auth B] S [auth B] H [auth A], I [auth A], K [auth A], R [auth B], S [auth B], T [auth B]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₇ H₁₀ O₅ JXOHGGNKMLTUBP-HSUXUTPPSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
3DS (Subject of Investigation/LOI) Query on 3DS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B]	G [auth A], Q [auth B]	(4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid C₇ H₈ O₅ SLWWJZMPHJJOPH-PHDIDXHHSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B]	E [auth A], O [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth B]	F [auth A], J [auth A], L [auth A], P [auth B], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain U [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B]	D [auth A], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]