Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis

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Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis is …
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scholarly articleQ13442814

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P356DOI10.1002/PROT.22936
P932PMC publication ID3065352
P698PubMed publication ID21287625
P5875ResearchGate publication ID49804333

P50authorJacquelyn S FetrowQ30505217
Laura SoitoQ38360700
Leslie B PooleQ59677915
P2093author name stringKimberly J Nelson
Chananat Klomsiri
Stacy T Knutson
P2860cites workAnnotation error in public databases: misannotation of molecular function in enzyme superfamiliesQ21145347
GenBankQ22065976
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceQ24286950
The Protein Data BankQ24515306
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymesQ24564680
Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxinQ24598311
Profile analysis: detection of distantly related proteinsQ24606115
PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin familyQ24615264
Enzyme-specific profiles for genome annotation: PRIAMQ24642072
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifsQ24671990
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificityQ24794945
Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like proteinQ27637390
The tetrameric structure of Haemophilus influenza hybrid Prx5 reveals interactions between electron donor and acceptor proteinsQ27640319
Peroxiredoxin evolution and the regulation of hydrogen peroxide signalingQ27641054
The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kineticsQ27641305
Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structuresQ27655652
Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State StabilizationQ27663573
Clustal W and Clustal X version 2.0Q27860517
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactionsQ27861128
Essential role for the peroxiredoxin Prdx1 in erythrocyte antioxidant defence and tumour suppressionQ28191015
Structure, mechanism and regulation of peroxiredoxinsQ28202120
Exhaustive matching of the entire protein sequence databaseQ28263532
Redox control in trypanosomatids, parasitic protozoa with trypanothione-based thiol metabolismQ28275518
PROSITE: a dictionary of sites and patterns in proteinsQ28280552
Bacterial defenses against oxidants: mechanistic features of cysteine-based peroxidases and their flavoprotein reductasesQ28296850
Thioredoxin-dependent hydroperoxide peroxidase activity of bacterioferritin comigratory protein (BCP) as a new member of the thiol-specific antioxidant protein (TSA)/Alkyl hydroperoxide peroxidase C (AhpC) familyQ28369099
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approachQ29036401
Reconciling the chemistry and biology of reactive oxygen speciesQ29615709
A motif-based profile scanning approach for genome-wide prediction of signaling pathwaysQ30168316
A quantitative methodology for the de novo design of proteinsQ30419165
Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structuresQ30422104
Recognition of spatial motifs in protein structuresQ30432556
Estimating the annotation error rate of curated GO database sequence annotationsQ33285442
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.Q33578211
Peroxiredoxin II is essential for sustaining life span of erythrocytes in mice.Q34177178
Protein fold recognition by prediction-based threadingQ34433804
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage databaseQ34496170
PeroxiredoxinsQ34523483
Hydrogen peroxide sensing and signalingQ34619087
Methods and statistics for combining motif match scoresQ34749635
Active site profiling to identify protein functional sites in sequences and structures using the Deacon Active Site Profiler (DASP).Q34772646
Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxinsQ35075095
Oxidation state governs structural transitions in peroxiredoxin II that correlate with cell cycle arrest and recoveryQ36119402
The plant multigenic family of thiol peroxidasesQ36125293
Prediction of membrane-protein topology from first principlesQ36734699
The catalytic mechanism of peroxiredoxins.Q37033954
Typical 2-Cys peroxiredoxins--structures, mechanisms and functions.Q37354876
ConFunc--functional annotation in the twilight zoneQ38514406
PRINTS--a database of protein motif fingerprints.Q40401046
Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidaseQ40676497
Contribution of the Helicobacter pylori thiol peroxidase bacterioferritin comigratory protein to oxidative stress resistance and host colonizationQ40735595
Prediction and evaluation of side-chain conformations for protein backbone structuresQ40921775
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.Q41594893
Four thiol peroxidases contain a conserved GCT catalytic motif and act as a versatile array of lipid peroxidases in Anabaena sp. PCC7120.Q42618386
Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestorQ42639363
Whole-genome sequence annotation: 'Going wrong with confidence'.Q43428325
An NADH-dependent bacterial thioredoxin reductase-like protein in conjunction with a glutaredoxin homologue form a unique peroxiredoxin (AhpC) reducing system in Clostridium pasteurianum.Q43876698
Identity and functions of CxxC-derived motifsQ44592443
Characterization of the yeast peroxiredoxin Ahp1 in its reduced active and overoxidized inactive forms using NMR.Q44670371
Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeastQ44674184
Poplar peroxiredoxin Q. A thioredoxin-linked chloroplast antioxidant functional in pathogen defenseQ44771713
The difficulty of annotating genes: the case of putrescine carbamoyltransferaseQ45176718
Crystal structure of a novel Plasmodium falciparum 1-Cys peroxiredoxinQ45257997
Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stressQ46484181
Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1.Q46743374
Preference functions for prediction of membrane-buried helices in integral membrane proteinsQ47780596
Go hunting in sequence databases but watch out for the trapsQ48059454
Thioredoxin-linked "thiol peroxidase" from periplasmic space of Escherichia coliQ48069055
Dimers to doughnuts: redox-sensitive oligomerization of 2-cysteine peroxiredoxins.Q50110017
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.Q52210980
Structure-based Active Site Profiles for Genome Analysis and Functional Family SubclassificationQ54981024
'Going wrong with confidence': misleading sequence analyses of CiaB and ClpXQ57017461
Chemical and Structural Diversity in Cyclooxygenase Protein Active SitesQ57275597
Editorial Commentary: Trichomonas vaginalisInfection: The Most Prevalent Nonviral Sexually Transmitted Infection Receives the Least Public Health AttentionQ58835994
What we do not know about sequence analysis and sequence databasesQ60309515
An approach to improving multiple alignments of protein sequences using predicted secondary structureQ73967920
The high reactivity of peroxiredoxin 2 with H(2)O(2) is not reflected in its reaction with other oxidants and thiol reagentsQ79847450
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)947-964
P577publication date2010-12-22
P1433published inProteinsQ7251514
P1476titleAnalysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis
P478volume79

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cites work (P2860)
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