6C4C

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

PDB DOI: https://doi.org/10.2210/pdb6C4C/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: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.192
R-Value Observed: 0.193

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: 392.73 kDa
Atom Count: 28,165
Modelled Residue Count: 3,421
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3NP Query on 3NP Download Ideal Coordinates CCD File SDF format, chain X [auth E] MOL2 format, chain X [auth E] mmCIF format, chain X [auth E]	X [auth E]	3-NITROPROPANOIC ACID C₃ H₅ N O₄ WBLZUCOIBUDNBV-UHFFFAOYSA-N		Interactions Focus chain X [auth E] Interactions & Density Focus chain X [auth E]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain U [auth E] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Y [auth F]	AA [auth G], L [auth B], O [auth C], U [auth E], Y [auth F]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain L [auth B] Focus chain O [auth C] Focus chain U [auth E] Focus chain Y [auth F]
GLV Query on GLV Download Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain R [auth D] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain R [auth D] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain R [auth D]	EA [auth H], I [auth A], R [auth D]	GLYOXYLIC ACID C₂ H₂ O₃ HHLFWLYXYJOTON-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Focus chain I [auth A] Focus chain R [auth D] Interactions & Density Focus chain EA [auth H] Focus chain I [auth A] Focus chain R [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth H] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	BA [auth G] CA [auth G] DA [auth H] FA [auth H] GA [auth H] BA [auth G], CA [auth G], DA [auth H], FA [auth H], GA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F]

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: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.76	α = 90
b = 87.13	β = 116.55
c = 152.99	γ = 90

Software Package:

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

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, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Refinement description
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations