2OE1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MITOCHONDRIAL THIOREDOXIN 3 FROM SACCHAROMYCES CEREVISIAE (REDUCED FORM)

Authors :   R. Bao, Y. R. Zhang, C. Z. Zhou, Y. X. Chen

Date :   28 Dec 06 (Deposition) - 08 Jan 08 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Electron Transport, Alpha/Beta Sandwich, Reduced, Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Bao, Y. R. Zhang, C. -Z. Zhou, Y. X. Chen
Structural And Mechanistic Analyses Of Yeast Mitochondrial Thioredoxin Trx3 Reveal Putative Function Of Its Additional Cysteine Residues
Biochim. Biophys. Acta V. 1794 716 2009
PubMed-ID: 19166985 | Reference-DOI: 10.1016/J.BBAPAP.2008.12.016
(for further references see the PDB file header)

Molecule 1 - THIOREDOXIN-3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET28A(MODIFIED)
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	TRX3
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	S288C

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:31 , LYS A:36 , PHE B:13 , ARG B:14 , GLU B:68 , LEU B:85 , HOH B:1035	BINDING SITE FOR RESIDUE SO4 B 1001
2	AC2	SOFTWARE	PHE A:13 , ARG A:14 , ILE A:17 , GLU A:68 , TRP B:31 , LYS B:36	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	THR A:11 , ARG A:14 , ASN A:15 , LYS B:44	BINDING SITE FOR RESIDUE SO4 A 1003

(no "SS Bond" information available for 2OE1)

Asymmetric/Biological Unit

No.	Residues
1	Met A:74	-	Pro A:75
2	Met B:74	-	Pro B:75

(no "SAP(SNP)/Variant" information available for 2OE1)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TRX3_YEAST	47-65	2	A:24-42 B:24-42

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YCR083W	1	YCR083W.1	III:259575-259958	384	TRX3_YEAST	1-127	127	2	A:-1-104 B:-1-104	106 106

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
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Chain A from PDB  Type:PROTEIN  Length:106
 aligned with TRX3_YEAST | P25372 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:106
                                    31        41        51        61        71        81        91       101       111       121      
           TRX3_YEAST    22 SSYTSITKLTNLTEFRNLIKQNDKLVIDFYATWCGPCKMMQPHLTKLIQAYPDVRFVKCDVDESPDIAKECEVTAMPTFVLGKDGQLIGKIIGANPTALEKGIKDL 127
               SCOP domains d2oe1a_ A: automated matches                                                                               SCOP domains
               CATH domains 2oe1A00 A:-1-104 Glutaredoxin                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeee...eeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      -------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:-1-104 UniProt: 1-127 [INCOMPLETE]                                                        Transcript 1
                 2oe1 A  -1 SSYTSITKLTNLTEFRNLIKQNDKLVIDFYATWCGPCKMMQPHLTKLIQAYPDVRFVKCDVDESPDIAKECEVTAMPTFVLGKDGQLIGKIIGANPTALEKGIKDL 104
                                     8        18        28        38        48        58        68        78        88        98

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with TRX3_YEAST | P25372 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:106
                                    31        41        51        61        71        81        91       101       111       121      
           TRX3_YEAST    22 SSYTSITKLTNLTEFRNLIKQNDKLVIDFYATWCGPCKMMQPHLTKLIQAYPDVRFVKCDVDESPDIAKECEVTAMPTFVLGKDGQLIGKIIGANPTALEKGIKDL 127
               SCOP domains d2oe1b_ B: automated matches                                                                               SCOP domains
               CATH domains 2oe1B00 B:-1-104 Glutaredoxin                                                                              CATH domains
           Pfam domains (1) -----Thioredoxin-2oe1B01 B:4-104                                                                           Pfam domains (1)
           Pfam domains (2) -----Thioredoxin-2oe1B02 B:4-104                                                                           Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      -------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:-1-104 UniProt: 1-127 [INCOMPLETE]                                                        Transcript 1
                 2oe1 B  -1 SSYTSITKLTNLTEFRNLIKQNDKLVIDFYATWCGPCKMMQPHLTKLIQAYPDVRFVKCDVDESPDIAKECEVTAMPTFVLGKDGQLIGKIIGANPTALEKGIKDL 104
                                     8        18        28        38        48        58        68        78        88        98

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: automated matches (347)

Protein domain: automated matches (347)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (13)

1a	d2oe1a_	A:
1b	d2oe1b_	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)

Baker's yeast (Saccharomyces cerevisiae) (19)

1a	2oe1A00	A:-1-104
1b	2oe1B00	B:-1-104

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin (82)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	Thioredoxin-2oe1B01	B:4-104
1b	Thioredoxin-2oe1B02	B:4-104

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TRX3_YEAST | P25372)

molecular function
	GO:0015036	disulfide oxidoreductase activity	Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (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.
	GO:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	2oe1
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	TRX3_YEAST \| P25372	:	2oe0 2oe3

2oe0	THE OXIDIZED AND REDUCED FORMS OF THE SAME PROTEIN
2oe3	THE SAME PROTEIN OXIDIZED WITH DIAMIDE

Description

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Ligands, Modified Residues, Ions (1, 3)

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SS Bonds (0, 0)

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