6C4A

Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with pyruvate

PDB DOI: https://doi.org/10.2210/pdb6C4A/pdb

Classification: LYASE
Organism(s): Mycobacterium tuberculosis str. Erdman = ATCC 35801
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-11 Released: 2018-06-06
Deposition Author(s): Kreitler, D.F., Ray, S., Murkin, A.S., Gulick, A.M.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.163

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition.

Ray, S., Kreitler, D.F., Gulick, A.M., Murkin, A.S.

(2018) ACS Chem Biol 13: 1470-1473

PubMed: 29782144 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acschembio.8b00225
Primary Citation of Related Structures:
6C4A, 6C4C

PubMed Abstract:
We report the unprecedented reaction between a nitroalkane and an active-site cysteine residue to yield a thiohydroximate adduct. Structural and kinetic evidence suggests the nitro group is activated by conversion to its nitronic acid tautomer within the active site. The nitro group, therefore, shows promise as a masked electrophile in the design of covalent inhibitors targeting binding pockets with appropriately placed cysteine and general acid residues.

Organizational Affiliation

Department of Chemistry , University at Buffalo , Buffalo , New York 14260-3000 , United States.

Macromolecule Content

Total Structure Weight: 394.23 kDa
Atom Count: 29,473
Modelled Residue Count: 3,423
Deposited Residue Count: 3,536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase 1	A, B, C, D, E A, B, C, D, E, F, G, H	442	Mycobacterium tuberculosis str. Erdman = ATCC 35801	Mutation(s): 0 Gene Names: icl1, ERDMAN_0512, Q643_00485 EC: 4.1.3.1 (PDB Primary Data), 4.1.3.30 (PDB Primary Data)
UniProt
Find proteins for P9WKK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKK7 Go to UniProtKB: P9WKK7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WKK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain MA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain MA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain MA [auth G]	EA [auth F], MA [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain MA [auth G] Interactions & Density Focus chain EA [auth F] Focus chain MA [auth G]
3NP Query on 3NP Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth C] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C]	M [auth B], V [auth C]	3-NITROPROPANOIC ACID C₃ H₅ N O₄ WBLZUCOIBUDNBV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth C] Interactions & Density Focus chain M [auth B] Focus chain V [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain JA [auth F] SDF format, chain OA [auth G] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain VA [auth H] SDF format, chain Z [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain Z [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain OA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain Z [auth D]	DA [auth E] JA [auth F] OA [auth G] Q [auth B] U [auth C] DA [auth E], JA [auth F], OA [auth G], Q [auth B], U [auth C], VA [auth H], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain JA [auth F] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain U [auth C] Focus chain VA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain JA [auth F] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain U [auth C] Focus chain VA [auth H] Focus chain Z [auth D]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain KA [auth G] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain RA [auth H] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain W [auth D]	AA [auth E] FA [auth F] I [auth A] KA [auth G] N [auth B] AA [auth E], FA [auth F], I [auth A], KA [auth G], N [auth B], R [auth C], RA [auth H], W [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain N [auth B] Focus chain R [auth C] Focus chain RA [auth H] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain N [auth B] Focus chain R [auth C] Focus chain RA [auth H] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain LA [auth G] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain QA [auth H] SDF format, chain S [auth C] SDF format, chain SA [auth H] SDF format, chain T [auth C] SDF format, chain TA [auth H] SDF format, chain UA [auth H] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain QA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	BA [auth E] CA [auth E] GA [auth F] HA [auth F] IA [auth F] BA [auth E], CA [auth E], GA [auth F], HA [auth F], IA [auth F], J [auth A], K [auth A], L [auth B], LA [auth G], NA [auth G], O [auth B], P [auth B], PA [auth G], QA [auth H], S [auth C], SA [auth H], T [auth C], TA [auth H], UA [auth H], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain LA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth G] Focus chain QA [auth H] Focus chain S [auth C] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain LA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth G] Focus chain QA [auth H] Focus chain S [auth C] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain X [auth D] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
EJA Query on EJA	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₆ H₁₀ N₂ O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.67	α = 90
b = 84.32	β = 116.59
c = 156.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE1255136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116957

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2018-06-27
Changes: Data collection, Database references
Version 2.0: 2022-03-16
Changes: Atomic model, Author supporting evidence, Database references, Derived calculations
Version 2.1: 2023-10-04
Changes: Data collection, Refinement description
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations