4Y1P | pdb_00004y1p

Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+

PDB DOI: https://doi.org/10.2210/pdb4Y1P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sulfolobus acidocaldarius DSM 639
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-08 Released: 2016-03-09
Deposition Author(s): Takahashi, K., Tomita, T., Kuzuyama, T., Nishiyama, M.
Funding Organization(s): Japan Society of the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.250 (Depositor), 0.231 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Characterization of two beta-decarboxylating dehydrogenases from Sulfolobus acidocaldarius

Takahashi, K., Nakanishi, F., Tomita, T., Akiyama, N., Lassak, K., Albers, S.V., Kuzuyama, T., Nishiyama, M.

(2016) Extremophiles 20: 843-853

PubMed: 27590116 Search on PubMed
DOI: https://doi.org/10.1007/s00792-016-0872-4
Primary Citation Related Structures:
4Y1P

PubMed Abstract:
Sulfolobus acidocaldarius, a hyperthermoacidophilic archaeon, possesses two β-decarboxylating dehydrogenase genes, saci_0600 and saci_2375, in its genome, which suggests that it uses these enzymes for three similar reactions in lysine biosynthesis through 2-aminoadipate, leucine biosynthesis, and the tricarboxylic acid cycle. To elucidate their roles, these two genes were expressed in Escherichia coli in the present study and their gene products were characterized. Saci_0600 recognized 3-isopropylmalate as a substrate, but exhibited slight and no activity for homoisocitrate and isocitrate, respectively. Saci_2375 exhibited distinct and similar activities for isocitrate and homoisocitrate, but no detectable activity for 3-isopropylmalate. These results suggest that Saci_0600 is a 3-isopropylmalate dehydrogenase for leucine biosynthesis and Saci_2375 is a dual function enzyme serving as isocitrate-homoisocitrate dehydrogenase. The crystal structure of Saci_0600 was determined as a closed-form complex that binds 3-isopropylmalate and Mg ²⁺, thereby revealing the structural basis for the extreme thermostability and novel-type recognition of the 3-isopropyl moiety of the substrate.

Organizational Affiliation

Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 73.64 kDa
Atom Count: 5,369
Modeled Residue Count: 671
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A, B	337	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0 Gene Names: leuB, Saci_0600 EC: 1.1.1.85
UniProt
Find proteins for Q4JB37 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4JB37 Go to UniProtKB: Q4JB37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4JB37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPM Query on IPM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	3-ISOPROPYLMALIC ACID C₇ H₁₂ O₅ RNQHMTFBUSSBJQ-CRCLSJGQSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.250 (Depositor), 0.231 (DCC)
R-Value Work: 0.190 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.024	α = 90
b = 136.719	β = 90
c = 112.519	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society of the Promotion of Science	Japan	24228001

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2016-12-14
Changes: Database references
Version 1.2: 2020-02-05
Changes: Data collection
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description