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Title :   CRYSTAL STRUCTURE OF A MAMMALIAN 2-CYS PEROXIREDOXIN, HBP23.

Authors :   S. Hirotsu, Y. Abe, K. Okada, N. Nagahara, H. Hori, T. Nishino, T. Hakoshima

Date :   10 Jun 99 (Deposition) - 29 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hirotsu, Y. Abe, K. Okada, N. Nagahara, H. Hori, T. Nishino, T. Hakoshima
Crystal Structure Of A Multifunctional 2-Cys Peroxiredoxin Heme-Binding Protein 23 Kda/Proliferation-Associated Gene Product.
Proc. Natl. Acad. Sci. Usa V. 96 12333 1999
PubMed-ID: 10535922 | Reference-DOI: 10.1073/PNAS.96.22.12333
(for further references see the PDB file header)

Molecule 1 - THIOREDOXIN PEROXIDASE 2
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organ	:	LIVER
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	HBP23 IN OXIDATIVE FORM REVEALED A UNIQUE DIMER STRUCTURE IN WHICH THE ACTIVE SITE CYSTEIN FORMS A DISULFIDE BOND WITH OTHER CYSTEIN FROM ANOTHER SUBUNIT.
	Synonym	:	HEME-BINDING PROTEIN 23 KD, HBP23

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:55 , ARG A:128 , HOH A:252	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	GLU B:55 , ARG B:128	BINDING SITE FOR RESIDUE CL B 302

Asymmetric/Biological Unit

No.	Residues
1	A:52	-	B:173
2	A:173	-	B:52

(no "Cis Peptide Bond" information available for 1QQ2)

(no "SAP(SNP)/Variant" information available for 1QQ2)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PRDX1_RAT	6-165	2	A:6-165 B:6-165

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000023132	1	ENSRNOE00000164803	chr5:136975761-136975821	61	PRDX1_RAT	-	0	0	-	-
1.2	ENSRNOT00000023132	2	ENSRNOE00000164845	chr5:136977666-136977782	117	PRDX1_RAT	1-36	36	2	A:3-36 B:3-36	34 34
1.3	ENSRNOT00000023132	3	ENSRNOE00000164920	chr5:136982758-136982911	154	PRDX1_RAT	36-87	52	2	A:36-87 B:36-87	52 52
1.4	ENSRNOT00000023132	4	ENSRNOE00000164960	chr5:136983328-136983450	123	PRDX1_RAT	87-128	42	2	A:87-128 B:87-128	42 42
1.5	ENSRNOT00000023132	5	ENSRNOE00000165006	chr5:136984963-136985093	131	PRDX1_RAT	128-172	45	2	A:128-172 B:128-172	45 45
1.6	ENSRNOT00000023132	6	ENSRNOE00000165051	chr5:136991313-136991633	321	PRDX1_RAT	172-199	28	2	A:172-175 B:172-175	4 4

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:173
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPA 175
               SCOP domains d1qq2a_ A: Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin)                                                                                           SCOP domains
               CATH domains 1qq2A00 A:3-175 Glutaredoxin                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee............hhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: A:6-165 UniProt: 6-165                                                                                                                      ---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: A:87-128 UniProt: 87-128   -------------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: A:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: A:128-172 UniProt: 128-172    --- Transcript 1 (2)
                 1qq2 A   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPA 175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPA 175
               SCOP domains d1qq2b_ B: Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin)                                                                                           SCOP domains
               CATH domains 1qq2B00 B:3-175 Glutaredoxin                                                                                                                                                  CATH domains
           Pfam domains (1) -----AhpC-TSA-1qq2B01 B:8-142                                                                                                               -------------------1-cysPrx_C-1qq Pfam domains (1)
           Pfam domains (2) -----AhpC-TSA-1qq2B02 B:8-142                                                                                                               -------------------1-cysPrx_C-1qq Pfam domains (2)
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee............hhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: B:6-165 UniProt: 6-165                                                                                                                      ---------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: B:87-128 UniProt: 87-128   -------------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: B:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: B:128-172 UniProt: 128-172    --- Transcript 1 (2)
                 1qq2 B   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPA 175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin) (3)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1qq2a_	A:
1b	d1qq2b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Norway rat (Rattus norvegicus) (10)

1a	1qq2A00	A:3-175
1b	1qq2B00	B:3-175

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: AhpC-TSA (28)

Rattus norvegicus (Rat) (1)

1a	AhpC-TSA-1qq2B01	B:8-142
1b	AhpC-TSA-1qq2B02	B:8-142

Clan: no clan defined [family: 1-cysPrx_C] (19)

Family: 1-cysPrx_C (19)

Rattus norvegicus (Rat) (1)

2a	1-cysPrx_C-1qq2B03	B:162-175
2b	1-cysPrx_C-1qq2B04	B:162-175

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PRDX1_RAT | Q63716)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005719	nuclear euchromatin	The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1QQ2)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (2, 2)

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