7KLD

Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a covalently linked product Peptide

PDB DOI: https://doi.org/10.2210/pdb7KLD/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-29 Released: 2021-09-01
Deposition Author(s): Wright, H.T., Peterson, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.279
R-Value Work: 0.245
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Phage-Related Ribosomal Protease (Prp) of Staphylococcus aureus : In Vitro Michaelis-Menten Kinetics, Screening for Inhibitors, and Crystal Structure of a Covalent Inhibition Product Complex.

Hotinger, J.A., Pendergrass, H.A., Peterson, D., Wright, H.T., May, A.E.

(2022) Biochemistry 61: 1323-1336

PubMed: 35731716 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.2c00010
Primary Citation of Related Structures:
7KLD

PubMed Abstract:
Phage-related ribosomal proteases (Prps) are essential for the assembly and maturation of the ribosome in Firmicutes, including the human pathogens Staphylococcus aureus , Streptococcus pneumoniae , and Clostridium difficile . These bacterial proteases cleave off an N-terminal extension of a precursor of ribosomal protein L27, a processing step that is essential for the formation of functional ribosomes. This essential role of Prp in these pathogens has identified this protease as a potential antibiotic target. In this work, we determine the X-ray crystal structure of a covalent inhibition complex at 2.35 Å resolution, giving the first complete picture of the active site of a functional Prp. We also characterize the kinetic activity and screen for potential inhibitors of Prp. This work gives the most complete characterization of the structure and specificity of this novel class of proteases to date.

Organizational Affiliation

Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, United States.

Macromolecule Content

Total Structure Weight: 38.25 kDa
Atom Count: 2,609
Modelled Residue Count: 332
Deposited Residue Count: 339
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-related ribosomal protease	A, B, D	106	Staphylococcus aureus	Mutation(s): 0 Gene Names: BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, E3K14_08315... BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, E3K14_08315, E4U00_05990, EP54_09330, EQ90_02345, ERS072840_00776, FA040_12870, FVP29_06750, G0V24_11265, G0X12_13445, G0X27_07880, G0Y02_04565, G0Z08_03095, G0Z18_03180, G6W67_00930, G6W97_12315, G6X24_04030, G6X31_01365, G6X35_09650, G6Y10_03065, G6Y24_01400, G6Y28_11445, G6Y30_16890, GF545_03610, GF559_00535, GIX97_04380, GO677_13485, GO706_06595, GO746_11035, GO788_00935, GO793_02925, GO793_12515, GO803_01985, GO805_05045, GO810_16085, GO821_00235, GO894_13395, GO915_03870, GO941_09805, GO942_04925, HMPREF3211_01798, M1K003_1397, NCTC10654_01710, NCTC10702_02585, NCTC5664_03624, NCTC6133_02188, NCTC7878_03165, RK64_08805, SAMEA1029528_01686, SAMEA1029547_02076, SAMEA1029553_02519, SAMEA1469856_00607, SAMEA1469884_01223, SAMEA1531680_00288, SAMEA1531701_01205, SAMEA1964876_02447, SAMEA1965205_02481, SAMEA1966505_02490, SAMEA1969349_02416, SAMEA1969845_01676, SAMEA1971706_01055, SAMEA1972827_01838, SAMEA2076212_01600, SAMEA2076218_01666, SAMEA2076220_01752, SAMEA2076226_01556, SAMEA2076463_02381, SAMEA2076464_02394, SAMEA2076470_02431, SAMEA2076472_02346, SAMEA2076478_02402, SAMEA2076480_02456, SAMEA2076481_02468, SAMEA2076743_02501, SAMEA2076745_02445, SAMEA2076746_02444, SAMEA2076747_02486, SAMEA2076749_02400, SAMEA2076751_02425, SAMEA2076752_02493, SAMEA2076755_02464, SAMEA2076756_02514, SAMEA2076758_02521, SAMEA2076759_02515, SAMEA2076761_02557, SAMEA2076762_01945, SAMEA2076763_01877, SAMEA2076764_02486, SAMEA2076765_02396, SAMEA2077023_02451, SAMEA2077025_02500, SAMEA2077027_02451, SAMEA2077029_02463, SAMEA2077031_02497, SAMEA2077034_01994, SAMEA2077035_02483, SAMEA2077039_02486, SAMEA2077040_02404, SAMEA2077041_02447, SAMEA2077044_02452, SAMEA2077045_02427, SAMEA2077046_02417, SAMEA2077293_02510, SAMEA2077294_02438, SAMEA2077295_02425, SAMEA2077297_02396, SAMEA2077300_02477, SAMEA2077301_02476, SAMEA2077302_02443, SAMEA2077303_02458, SAMEA2077307_02357, SAMEA2077832_02485, SAMEA2078252_02489, SAMEA2078256_02457, SAMEA2078307_02502, SAMEA2078308_02409, SAMEA2078553_02399, SAMEA2078558_02472, SAMEA2078560_02496, SAMEA2078569_00046, SAMEA2078570_02413, SAMEA2078572_02514, SAMEA2078824_02435, SAMEA2078837_02548, SAMEA2079048_02570, SAMEA2079051_02465, SAMEA2079277_01808, SAMEA2079291_02682, SAMEA2079503_02553, SAMEA2079507_01005, SAMEA2079512_02667, SAMEA2079517_02674, SAMEA2079724_01337, SAMEA2079727_01612, SAMEA2079728_01943, SAMEA2079732_01656, SAMEA2079742_01684, SAMEA2079946_01624, SAMEA2079949_01591, SAMEA2079951_01555, SAMEA2079952_01419, SAMEA2079957_01912, SAMEA2079958_01822, SAMEA2079960_01835, SAMEA2079961_01609, SAMEA2079968_01340, SAMEA2080329_01468, SAMEA2080330_01912, SAMEA2080334_01932, SAMEA2080433_01740, SAMEA2080812_02522, SAMEA2080898_02518, SAMEA2080900_02445, SAMEA2080904_02459, SAMEA2080913_02507, SAMEA2081043_02492, SAMEA2081053_02569, SAMEA2081054_02533, SAMEA2081055_02521, SAMEA2081060_01823, SAMEA2081211_00857, SAMEA2081213_00881, SAMEA2081218_01649, SAMEA2081341_01341, SAMEA2081342_01612, SAMEA2081349_01864, SAMEA2081359_01619, SAMEA2081362_01623, SAMEA2081468_02419, SAMEA2081474_02496, SAMEA2081475_02467, SAMEA2081476_02433, SAMEA2081479_02517, SAMEA2081480_02464, SAMEA2081560_02361, SAMEA2081561_02437, SAMEA2081564_02416, SAMEA2081567_02404, SAMEA2081568_02500, SAMEA2081569_02476, SAMEA2081570_02367, SAMEA2081571_02441, SAMEA2081572_02441, SAMEA2081573_02444, SAMEA2081575_02417, SAMEA2081577_02472, SAMEA2081578_02440, SAMEA2081579_02464, SAMEA2081581_02376, SAMEA2081582_02553, SAMEA2081673_01456, SAMEA2081674_01693, SAMEA958766_01141, SAMEA958770_01541, SAMEA958772_01367, SAMEA958778_01377, SAMEA958779_02720, SAMEA958785_01190, SAMEA958793_01565, SAMEA958798_01254, SAMEA958804_01429, SAMEA958810_02901, SAMEA958836_01614, SAMEA958838_02812, SAMEA958845_01498, SAMEA958846_01744, SAMEA958848_02333, SAMEA958855_02126, SAMEA958858_02293, SAMEA958870_02489, SAMEA958898_01783, SAMEA958906_02170, SAMEA958924_01277, SAMEA958925_01299, SAMEA958951_01296, SAMEA958953_00896, SAMEA958961_01996, SAMEA958979_01146, SAMEA958987_02151, SAMEA958995_01155, SAST44_01826, SAST45_01804
UniProt
Find proteins for Q2FXS9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXS9 Go to UniProtKB: Q2FXS9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXS9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-LEU-ASN-LEU-GLN-PHE-PCS	C, E, F [auth Q]	7	Staphylococcus aureus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth D], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCS Query on PCS	C, E, F [auth Q]	L-PEPTIDE LINKING	C₁₀ H₁₂ Cl N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002454 Query on PRD_002454	C, E, F [auth Q]	Substrate-like cysteine protease inhibitor	Peptide-like / Inhibitor		Interactions Focus chain C Focus chain E Focus chain F [auth Q] Interactions & Density Focus chain C Focus chain E Focus chain F [auth Q]