EzCatDB: D00870
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DB codeD00870
RLCP classification3.676.249900.37 : Transfer
CATH domainDomain 13.40.30.10 : GlutaredoxinCatalytic domain
Domain 23.30.1020.10 : Antioxidant, Horf6; Chain A, domain 2
E.C.1.11.1.15

CATH domainRelated DB codes (homologues)
3.40.30.10 : GlutaredoxinS00916,S00279,M00184,D00866,D00869,D00278

Enzyme Name
UniProtKBKEGG

Q86SB3
Protein name
Peroxiredoxin
Thioredoxin peroxidase
Tryparedoxin peroxidase
Alkyl hydroperoxide reductase C22
AhpC
TrxPx
TXNPx
Prx
PRDX
Synonyms1-Cys peroxiredoxin
PfamPF10417 (1-cysPrx_C)
PF00578 (AhpC-TSA)
[Graphical view]


UniProtKB:Accession NumberQ86SB3
Entry nameQ86SB3_9APIC
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC16736C15498C15496C00001C01335I00142I00143
CompoundR'-SHROOHR-S-S-RH2OROHPeptidyl-Cys-sulfenic acidTransient disulfide bond between peptidyl-Cys
Typesulfhydryl groupothersdisulfide bondH2Ocarbohydrate

ChEBI


15377



PubChem


962
22247451



               
1xccA01UnboundUnboundUnbound UnboundUnboundUnbound
1xccB01UnboundUnboundUnbound UnboundUnboundUnbound
1xccC01UnboundUnboundUnbound UnboundUnboundUnbound
1xccD01UnboundUnboundUnbound UnboundUnboundUnbound
3tb2A01UnboundUnboundUnbound UnboundIntermediate-analogue:CSDUnbound
3tb2B01UnboundUnboundUnbound UnboundIntermediate-analogue:CSDUnbound
3tb2C01UnboundUnboundUnbound UnboundIntermediate-analogue:CSDUnbound
3tb2D01UnboundUnboundUnbound UnboundIntermediate-analogue:CSDUnbound
1xccA02UnboundUnboundUnbound UnboundUnboundUnbound
1xccB02UnboundUnboundUnbound UnboundUnboundUnbound
1xccC02UnboundUnboundUnbound UnboundUnboundUnbound
1xccD02UnboundUnboundUnbound UnboundUnboundUnbound
3tb2A02UnboundUnboundUnbound UnboundUnboundUnbound
3tb2B02UnboundUnboundUnbound UnboundUnboundUnbound
3tb2C02UnboundUnboundUnbound UnboundUnboundUnbound
3tb2D02UnboundUnboundUnbound UnboundUnboundUnbound

Active-site residues
resource
Literature [1], [2], [4], [5], [6]
pdbCatalytic residuesModified residuesMain-chain involved in catalysis
           
1xccA01THR 44;CYS 47;ARG 129
                        
ASN 41;VAL 46;CYS 47
1xccB01THR 44;CYS 47;ARG 129
                        
ASN 41;VAL 46;CYS 47
1xccC01THR 44;CYS 47;ARG 129
                        
ASN 41;VAL 46;CYS 47
1xccD01THR 44;CYS 47;ARG 129
                        
ASN 41;VAL 46;CYS 47
3tb2A01THR 44;      ;ARG 129
CSD 47(3-Sulfinoalanine)
ASN 41;VAL 46;CYS 47
3tb2B01THR 44;      ;ARG 129
CSD 47(3-Sulfinoalanine)
ASN 41;VAL 46;CYS 47
3tb2C01THR 44;      ;ARG 129
CSD 47(3-Sulfinoalanine)
ASN 41;VAL 46;CYS 47
3tb2D01THR 44;      ;ARG 129
CSD 47(3-Sulfinoalanine)
ASN 41;VAL 46;CYS 47
1xccA02                     
 
 
1xccB02                     
 
 
1xccC02                     
 
 
1xccD02                     
 
 
3tb2A02                     
 
 
3tb2B02                     
 
 
3tb2C02                     
 
 
3tb2D02                     
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig. 4
[2]Fig. 1

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID9587003
JournalNat Struct Biol
Year1998
Volume5
Pages400-6
AuthorsChoi HJ, Kang SW, Yang CH, Rhee SG, Ryu SE
TitleCrystal structure of a novel human peroxidase enzyme at 2.0 A resolution.
Related PDB1prx
Related UniProtKBP30041
[2]
PubMed ID12517450
JournalTrends Biochem Sci
Year2003
Volume28
Pages32-40
AuthorsWood ZA, Schroder E, Robin Harris J, Poole LB
TitleStructure, mechanism and regulation of peroxiredoxins.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), SULFINATION AT CYS-47.
PubMed ID17125854
JournalMol Biochem Parasitol
Year2007
Volume151
Pages100-10
AuthorsVedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R
TitleGenome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Related PDB1xcc,3tb2
Related UniProtKBQ86SB3
[4]
PubMed ID18084889
JournalSubcell Biochem
Year2007
Volume44
Pages41-60
AuthorsKarplus PA, Hall A
TitleStructural survey of the peroxiredoxins.
[5]
PubMed ID20969484
JournalAntioxid Redox Signal
Year2011
Volume15
Pages795-815
AuthorsHall A, Nelson K, Poole LB, Karplus PA
TitleStructure-based insights into the catalytic power and conformational dexterity of peroxiredoxins.
[6]
PubMed ID22429898
JournalBMC Struct Biol
Year2012
Volume12
Pages2
AuthorsQiu W, Dong A, Pizarro JC, Botchkarsev A, Min J, Wernimont AK, Hills T, Hui R, Artz JD
TitleCrystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

comments
Peroxiredoxins (Prxs) can be classified into three categories (see [2]):
(1) typical 2-Cys Prxs; conservation of two redox-active cysteines; homodimers having two identical active sites.
(2) atypical 2-Cys Prxs; conservation of two redox-active cysteines; functionally monomeric.
(3) 1-Cys Prxs; only one cysteine.
This enzyme belongs to the category of 1-Cys Prxs.
The redox-active cysteine is referred to as the peroxidatic cysteine, in contrast to the second cysteine, the resolving cysteine, in the 2-Cys Prxs.
Since this enzyme is homologous to 1-Cys Prxs (D00869, S00916 in EzCatDB) with a similar active site, it must have a similar catalytic mechanism as the homologue.
Thus, this enzyme catalyzes the following reactions (see [2]):
(A) Transfer of peroxide oxygen from another peroxide oxygen to the perdoxidatic Cys, forming Cys-sulfenic acid:
(B) Transfer of sulfur atom of the peroxidatic Cys from the hydroxyl group to thiol (or sulfhydryl) group of the second substrat
(C) Electron transfer from thiol of the third substrate (or another R'-SH) to the disulfide bond (thiol-disulfide exchange):
Although this enzyme can be over-oxidized to form sulfinic acid (-SO2H) and further oxidized sulfonic acid (-SO3H), over-oxidization mechanism is not described in this entry. Incidentally, 3tb2 (of PDB) gives structures of sulfinic acid form.

createdupdated
2012-07-122012-09-13


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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