7LJ1 | pdb_00007lj1

Human Prx1-Srx Decameric Complex

PDB DOI: https://doi.org/10.2210/pdb7LJ1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-28 Released: 2021-07-14
Deposition Author(s): Forshaw, T.E., Reisz, J.A., Nelson, K.J., Gumpena, R., Lawson, J.R., Jonsson, T., Wu, H., Clodfelter, J.E., Johnson, L., Furdui, C.M., Lowther, W.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Specificity of Human Sulfiredoxin for Reductant and Peroxiredoxin Oligomeric State.

Forshaw, T.E., Reisz, J.A., Nelson, K.J., Gumpena, R., Lawson, J.R., Jonsson, T.J., Wu, H., Clodfelter, J.E., Johnson, L.C., Furdui, C.M., Lowther, W.T.

(2021) Antioxidants (Basel) 10

PubMed: 34208049 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/antiox10060946
Primary Citation Related Structures:
7LJ1

PubMed Abstract:
Human peroxiredoxins (Prx) are a family of antioxidant enzymes involved in a myriad of cellular functions and diseases. During the reaction with peroxides (e.g., H ₂O ₂), the typical 2-Cys Prxs change oligomeric structure between higher order (do)decamers and disulfide-linked dimers, with the hyperoxidized inactive state (-SO ₂H) favoring the multimeric structure of the reduced enzyme. Here, we present a study on the structural requirements for the repair of hyperoxidized 2-Cys Prxs by human sulfiredoxin (Srx) and the relative efficacy of physiological reductants hydrogen sulfide (H ₂S) and glutathione (GSH) in this reaction. The crystal structure of the toroidal Prx1-Srx complex shows an extended active site interface. The loss of this interface within engineered Prx2 and Prx3 dimers yielded variants more resistant to hyperoxidation and repair by Srx. Finally, we reveal for the first time Prx isoform-dependent use of and potential cooperation between GSH and H ₂S in supporting Srx activity.

Organizational Affiliation

Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157, USA.

Macromolecule Content

Total Structure Weight: 684.84 kDa
Atom Count: 44,942
Modeled Residue Count: 5,782
Deposited Residue Count: 6,160
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-1	A C [auth B] D [auth C] E [auth D] F [auth E] A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q], S [auth R], T [auth S], U [auth T]	199	Homo sapiens	Mutation(s): 3 Gene Names: PRDX1, PAGA, PAGB, TDPX2 EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens) Explore Q06830 Go to UniProtKB: Q06830
PHAROS: Q06830 GTEx: ENSG00000117450
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06830
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfiredoxin-1	AA [auth g] B [auth a] BA [auth h] CA [auth i] DA [auth j] AA [auth g], B [auth a], BA [auth h], CA [auth i], DA [auth j], EA [auth k], FA [auth l], GA [auth m], HA [auth n], IA [auth o], JA [auth p], KA [auth q], LA [auth r], MA [auth s], NA [auth t], V [auth b], W [auth c], X [auth d], Y [auth e], Z [auth f]	109	Homo sapiens	Mutation(s): 0 Gene Names: SRXN1, C20orf139, SRX, SRX1 EC: 1.8.98.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYN0 (Homo sapiens) Explore Q9BYN0 Go to UniProtKB: Q9BYN0
PHAROS: Q9BYN0 GTEx: ENSG00000271303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain RB [auth c] SDF format, chain VB [auth g] MOL2 format, chain RB [auth c] MOL2 format, chain VB [auth g] mmCIF format, chain RB [auth c] mmCIF format, chain VB [auth g]	RB [auth c], VB [auth g]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain RB [auth c] Focus chain VB [auth g] Interactions & Density Focus chain RB [auth c] Focus chain VB [auth g]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CB [auth K] SDF format, chain DB [auth N] SDF format, chain EB [auth O] SDF format, chain IB [auth P] SDF format, chain KB [auth Q] SDF format, chain NB [auth R] SDF format, chain SA [auth D] SDF format, chain WA [auth G] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth N] MOL2 format, chain EB [auth O] MOL2 format, chain IB [auth P] MOL2 format, chain KB [auth Q] MOL2 format, chain NB [auth R] MOL2 format, chain SA [auth D] MOL2 format, chain WA [auth G] mmCIF format, chain CB [auth K] mmCIF format, chain DB [auth N] mmCIF format, chain EB [auth O] mmCIF format, chain IB [auth P] mmCIF format, chain KB [auth Q] mmCIF format, chain NB [auth R] mmCIF format, chain SA [auth D] mmCIF format, chain WA [auth G]	CB [auth K] DB [auth N] EB [auth O] IB [auth P] KB [auth Q] CB [auth K], DB [auth N], EB [auth O], IB [auth P], KB [auth Q], NB [auth R], SA [auth D], WA [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth K] Focus chain DB [auth N] Focus chain EB [auth O] Focus chain IB [auth P] Focus chain KB [auth Q] Focus chain NB [auth R] Focus chain SA [auth D] Focus chain WA [auth G] Interactions & Density Focus chain CB [auth K] Focus chain DB [auth N] Focus chain EB [auth O] Focus chain IB [auth P] Focus chain KB [auth Q] Focus chain NB [auth R] Focus chain SA [auth D] Focus chain WA [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AC [auth l] SDF format, chain BC [auth m] SDF format, chain CC [auth n] SDF format, chain DC [auth o] SDF format, chain EC [auth p] SDF format, chain FC [auth q] SDF format, chain GC [auth r] SDF format, chain HC [auth s] SDF format, chain IC [auth t] SDF format, chain PA [auth a] SDF format, chain QB [auth b] SDF format, chain SB [auth d] SDF format, chain TA [auth E] SDF format, chain TB [auth e] SDF format, chain UB [auth f] SDF format, chain WB [auth h] SDF format, chain XB [auth i] SDF format, chain YB [auth j] SDF format, chain ZB [auth k] MOL2 format, chain AC [auth l] MOL2 format, chain BC [auth m] MOL2 format, chain CC [auth n] MOL2 format, chain DC [auth o] MOL2 format, chain EC [auth p] MOL2 format, chain FC [auth q] MOL2 format, chain GC [auth r] MOL2 format, chain HC [auth s] MOL2 format, chain IC [auth t] MOL2 format, chain PA [auth a] MOL2 format, chain QB [auth b] MOL2 format, chain SB [auth d] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth e] MOL2 format, chain UB [auth f] MOL2 format, chain WB [auth h] MOL2 format, chain XB [auth i] MOL2 format, chain YB [auth j] MOL2 format, chain ZB [auth k] mmCIF format, chain AC [auth l] mmCIF format, chain BC [auth m] mmCIF format, chain CC [auth n] mmCIF format, chain DC [auth o] mmCIF format, chain EC [auth p] mmCIF format, chain FC [auth q] mmCIF format, chain GC [auth r] mmCIF format, chain HC [auth s] mmCIF format, chain IC [auth t] mmCIF format, chain PA [auth a] mmCIF format, chain QB [auth b] mmCIF format, chain SB [auth d] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth e] mmCIF format, chain UB [auth f] mmCIF format, chain WB [auth h] mmCIF format, chain XB [auth i] mmCIF format, chain YB [auth j] mmCIF format, chain ZB [auth k]	AC [auth l] BC [auth m] CC [auth n] DC [auth o] EC [auth p] AC [auth l], BC [auth m], CC [auth n], DC [auth o], EC [auth p], FC [auth q], GC [auth r], HC [auth s], IC [auth t], PA [auth a], QB [auth b], SB [auth d], TA [auth E], TB [auth e], UB [auth f], WB [auth h], XB [auth i], YB [auth j], ZB [auth k]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AC [auth l] Focus chain BC [auth m] Focus chain CC [auth n] Focus chain DC [auth o] Focus chain EC [auth p] Focus chain FC [auth q] Focus chain GC [auth r] Focus chain HC [auth s] Focus chain IC [auth t] Focus chain PA [auth a] Focus chain QB [auth b] Focus chain SB [auth d] Focus chain TA [auth E] Focus chain TB [auth e] Focus chain UB [auth f] Focus chain WB [auth h] Focus chain XB [auth i] Focus chain YB [auth j] Focus chain ZB [auth k] Interactions & Density Focus chain AC [auth l] Focus chain BC [auth m] Focus chain CC [auth n] Focus chain DC [auth o] Focus chain EC [auth p] Focus chain FC [auth q] Focus chain GC [auth r] Focus chain HC [auth s] Focus chain IC [auth t] Focus chain PA [auth a] Focus chain QB [auth b] Focus chain SB [auth d] Focus chain TA [auth E] Focus chain TB [auth e] Focus chain UB [auth f] Focus chain WB [auth h] Focus chain XB [auth i] Focus chain YB [auth j] Focus chain ZB [auth k]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain GB [auth O] SDF format, chain XA [auth H] MOL2 format, chain GB [auth O] MOL2 format, chain XA [auth H] mmCIF format, chain GB [auth O] mmCIF format, chain XA [auth H]	GB [auth O], XA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GB [auth O] Focus chain XA [auth H] Interactions & Density Focus chain GB [auth O] Focus chain XA [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth J] SDF format, chain FB [auth O] SDF format, chain HB [auth P] SDF format, chain JB [auth Q] SDF format, chain LB [auth R] SDF format, chain MB [auth R] SDF format, chain OA [auth A] SDF format, chain OB [auth S] SDF format, chain PB [auth S] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth J] MOL2 format, chain FB [auth O] MOL2 format, chain HB [auth P] MOL2 format, chain JB [auth Q] MOL2 format, chain LB [auth R] MOL2 format, chain MB [auth R] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth S] MOL2 format, chain PB [auth S] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] mmCIF format, chain AB [auth H] mmCIF format, chain BB [auth J] mmCIF format, chain FB [auth O] mmCIF format, chain HB [auth P] mmCIF format, chain JB [auth Q] mmCIF format, chain LB [auth R] mmCIF format, chain MB [auth R] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth S] mmCIF format, chain PB [auth S] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H]	AB [auth H] BB [auth J] FB [auth O] HB [auth P] JB [auth Q] AB [auth H], BB [auth J], FB [auth O], HB [auth P], JB [auth Q], LB [auth R], MB [auth R], OA [auth A], OB [auth S], PB [auth S], QA [auth C], RA [auth C], UA [auth G], VA [auth G], YA [auth H], ZA [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth J] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain JB [auth Q] Focus chain LB [auth R] Focus chain MB [auth R] Focus chain OA [auth A] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth J] Focus chain FB [auth O] Focus chain HB [auth P] Focus chain JB [auth Q] Focus chain LB [auth R] Focus chain MB [auth R] Focus chain OA [auth A] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain YA [auth H] Focus chain ZA [auth H]