6UA2

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Bent (2/4 compressed, 2/4 extended) segment reconstruction.

PDB DOI: https://doi.org/10.2210/pdb6UA2/pdb
EM Map EMD-20687: EMDB EMDataResource
EM Map EMD-20688: EMDB EMDataResource
EM Map EMD-20690: EMDB EMDataResource
EM Map EMD-20691: EMDB EMDataResource
EM Map EMD-20701: EMDB EMDataResource
EM Map EMD-20704: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-10 Released: 2020-03-25
Deposition Author(s): Johnson, M.C., Kollman, J.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.

Johnson, M.C., Kollman, J.M.

(2020) Elife 9

PubMed: 31999252 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.53243
Primary Citation of Related Structures:
6U8E, 6U8N, 6U8R, 6U8S, 6U9O, 6UA2, 6UA4, 6UA5, 6UAJ, 6UC2, 6UDO, 6UDP, 6UDQ

PubMed Abstract:
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.

Organizational Affiliation

Department of Biochemistry, University of Washington, Seattle, United States.

Macromolecule Content

Total Structure Weight: 922.05 kDa
Atom Count: 31,660
Modelled Residue Count: 4,016
Deposited Residue Count: 8,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase 2	A B C D E [auth M] A, B, C, D, E [auth M], F [auth N], G [auth O], H [auth P], I [auth E], J [auth F], K [auth G], L [auth H], M [auth I], N [auth J], O [auth K], P [auth L]	519	Homo sapiens	Mutation(s): 0 Gene Names: IMPDH2, IMPD2 EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens) Explore P12268 Go to UniProtKB: P12268
PHAROS: P12268 GTEx: ENSG00000178035
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12268
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 HA [auth D] SDF format, chain MA [auth E] SDF format, chain RA [auth F] SDF format, chain U [auth A] SDF format, chain Z [auth B] SDF format, chain ZA [auth H] SDF format, chain DA [auth C] SDF format, chain WA [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain WA [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain RA [auth F] mmCIF format, chain U [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth H] mmCIF format, chain DA [auth C] mmCIF format, chain WA [auth G]	DA [auth C] HA [auth D] MA [auth E] RA [auth F] U [auth A] DA [auth C], HA [auth D], MA [auth E], RA [auth F], U [auth A], WA [auth G], Z [auth B], ZA [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain DA [auth C] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain RA [auth F] Focus chain U [auth A] Focus chain WA [auth G] Focus chain Z [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain DA [auth C] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain RA [auth F] Focus chain U [auth A] Focus chain WA [auth G] Focus chain Z [auth B] Focus chain ZA [auth H]
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain NA [auth F] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain OA [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain OA [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain OA [auth F]	IA [auth E] JA [auth E] NA [auth F] OA [auth F] Q [auth A] IA [auth E], JA [auth E], NA [auth F], OA [auth F], Q [auth A], R [auth A], V [auth B], W [auth B]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain IA [auth E] Focus chain JA [auth E] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain IA [auth E] Focus chain JA [auth E] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] SDF format, chain KA [auth E] SDF format, chain PA [auth F] SDF format, chain S [auth A] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain X [auth B] SDF format, chain XA [auth H] SDF format, chain BA [auth C] SDF format, chain EA [auth C] SDF format, chain UA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain UA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain KA [auth E] mmCIF format, chain PA [auth F] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain UA [auth G]	AA [auth C] BA [auth C] EA [auth C] FA [auth D] KA [auth E] AA [auth C], BA [auth C], EA [auth C], FA [auth D], KA [auth E], PA [auth F], S [auth A], SA [auth G], TA [auth G], UA [auth G], X [auth B], XA [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain KA [auth E] Focus chain PA [auth F] Focus chain S [auth A] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain X [auth B] Focus chain XA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain KA [auth E] Focus chain PA [auth F] Focus chain S [auth A] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain X [auth B] Focus chain XA [auth H]
IMP (Subject of Investigation/LOI) Query on IMP Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain LA [auth E] SDF format, chain T [auth A] SDF format, chain VA [auth G] SDF format, chain Y [auth B] SDF format, chain YA [auth H] SDF format, chain CA [auth C] SDF format, chain QA [auth F] MOL2 format, chain GA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain QA [auth F] mmCIF format, chain GA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain QA [auth F]	CA [auth C] GA [auth D] LA [auth E] QA [auth F] T [auth A] CA [auth C], GA [auth D], LA [auth E], QA [auth F], T [auth A], VA [auth G], Y [auth B], YA [auth H]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain CA [auth C] Focus chain GA [auth D] Focus chain LA [auth E] Focus chain QA [auth F] Focus chain T [auth A] Focus chain VA [auth G] Focus chain Y [auth B] Focus chain YA [auth H] Interactions & Density Focus chain CA [auth C] Focus chain GA [auth D] Focus chain LA [auth E] Focus chain QA [auth F] Focus chain T [auth A] Focus chain VA [auth G] Focus chain Y [auth B] Focus chain YA [auth H]