5HUQ

A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase

PDB DOI: https://doi.org/10.2210/pdb5HUQ/pdb
Entry: 5HUQ supersedes: 4YNS

Classification: ISOMERASE
Organism(s): Lactiplantibacillus plantarum
Expression System: Lactiplantibacillus plantarum
Mutation(s): No

Deposited: 2016-01-27 Released: 2016-02-10
Deposition Author(s): Desguin, B., Zhang, T., Soumillion, P., Hols, P., Hu, J., Hausinger, R.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 ?
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase.

Desguin, B., Zhang, T., Soumillion, P., Hols, P., Hu, J., Hausinger, R.P.

(2015) Science 349: 66-69

PubMed: 26138974 Search on PubMed
DOI: https://doi.org/10.1126/science.aab2272
Primary Citation of Related Structures:
5HUQ

PubMed Abstract:
Lactic acid racemization is involved in lactate metabolism and cell wall assembly of many microorganisms. Lactate racemase (Lar) requires nickel, but the nickel-binding site and the role of three accessory proteins required for its activation remain enigmatic. We combined mass spectrometry and x-ray crystallography to show that Lar from Lactobacillus plantarum possesses an organometallic nickel-containing prosthetic group. A nicotinic acid mononucleotide derivative is tethered to Lys(184) and forms a tridentate pincer complex that coordinates nickel through one metal-carbon and two metal-sulfur bonds, with His(200) as another ligand. Although similar complexes have been previously synthesized, there was no prior evidence for the existence of pincer cofactors in enzymes. The wide distribution of the accessory proteins without Lar suggests that it may play a role in other enzymes.

Organizational Affiliation

Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.

Macromolecule Content

Total Structure Weight: 97.71 kDa
Atom Count: 6,780
Modelled Residue Count: 865
Deposited Residue Count: 866
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactate racemization operon protein LarA	A, B	433	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: AB662_09960, ADS73_14595, AKJ11_11795, AN634_09100, AOZ08_01600, IV39_GL000121, JM48_0086, Nizo2877_0389, WU67_00115 EC: 5.1.2.1
UniProt
Find proteins for F9USS9 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9USS9 Go to UniProtKB: F9USS9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9USS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4EY Query on 4EY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium C₁₂ H₁₅ N O₈ P S₂ NSIYRWZYSRADIJ-GWOFURMSSA-O		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] D [auth A] E [auth A] F [auth A] AA [auth B], BA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 ?
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 111.277	α = 90
b = 111.277	β = 90
c = 306.181	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

This entry supersedes: 4YNS

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 2.0: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2024-11-13
Changes: Structure summary