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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NDPPH DEPENDENT THIOREDOXIN REDUCTASE 1

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

Date :   26 May 08 (Deposition) - 09 Dec 08 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Thioredoxin Reductase, Nadph, Yeast, Modpipe Model Of A6Z, Fad, Flavoprotein, Oxidoreductase, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, R. Bao, Y. Zhang, J. Yu, C. -Z. Zhou, Y. Chen
Crystal Structure Of Saccharomyces Cerevisiae Cytoplasmic Thioredoxin Reductase Trr1 Reveals The Structural Basis For Species-Specific Recognition Of Thioredoxin
Biochim. Biophys. Acta V. 1794 124 2009
PubMed-ID: 18930846 | Reference-DOI: 10.1016/J.BBAPAP.2008.09.011

Molecule 1 - THIOREDOXIN REDUCTASE 1
	Chains	:	A, B
	EC Number	:	1.8.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRR1
	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 (2, 3)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:9 , GLY A:10 , SER A:11 , GLY A:12 , PRO A:13 , ALA A:14 , TYR A:32 , GLU A:33 , GLY A:34 , ALA A:37 , ILE A:40 , ALA A:41 , GLY A:44 , GLN A:45 , LEU A:46 , ILE A:52 , ASN A:54 , THR A:86 , THR A:119 , GLY A:120 , TRP A:135 , CYS A:145 , GLY A:287 , ASP A:288 , ARG A:295 , GLN A:296 , ALA A:297 , SER A:300 , TYR B:21	BINDING SITE FOR RESIDUE FAD A 1001
2	AC2	SOFTWARE	TYR A:21 , ILE B:9 , GLY B:10 , SER B:11 , GLY B:12 , PRO B:13 , ALA B:14 , TYR B:32 , GLU B:33 , GLY B:34 , ALA B:37 , ILE B:40 , ALA B:41 , GLY B:44 , GLN B:45 , LEU B:46 , THR B:49 , ILE B:52 , ASN B:54 , THR B:119 , GLY B:120 , TRP B:135 , CYS B:145 , GLY B:287 , ASP B:288 , ARG B:295 , GLN B:296 , ALA B:297 , SER B:300	BINDING SITE FOR RESIDUE FAD B 1001
3	AC3	SOFTWARE	MET A:126 , GLY A:161 , GLY A:163 , SER A:165 , ARG A:185 , LYS A:186 , ARG A:190 , ILE A:248 , ASP B:106	BINDING SITE FOR RESIDUE NDP A 481

Asymmetric/Biological Unit

No.	Residues
1	A:142	-	A:145
2	B:142	-	B:145

Asymmetric/Biological Unit

No.	Residues
1	Lys A:95	-	Pro A:96
2	Lys B:95	-	Pro B:96

(no "SAP(SNP)/Variant" information available for 3D8X)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_2	PS00573	Pyridine nucleotide-disulphide oxidoreductases class-II active site.	TRXB1_YEAST	142-164	2	A:142-164 B:142-164

(no "Exon" information available for 3D8X)

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:318
 aligned with TRXB1_YEAST | P29509 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
          TRXB1_YEAST     2 VHNKVTIIGSGPAAHTAAIYLARAEIKPILYEGMMANGIAAGGQLTTTTEIENFPGFPDGLTGSELMDRMREQSTKFGTEIITETVSKVDLSSKPFKLWTEFNEDAEPVTTDAIILATGASAKRMHLPGEETYWQKGISACAVCDGAVPIFRNKPLAVIGGGDSACEEAQFLTKYGSKVFMLVRKDHLRASTIMQKRAEKNEKIEILYNTVALEAKGDGKLLNALRIKNTKKNEETDLPVSGLFYAIGHTPATKIVAGQVDTDEAGYIKTVPGSSLTSVPGFFAAGDVQDSKYRQAITSAGSGCMAALDAEKYLTSLE 319
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3d8xA01 A:2-123,A:250-317  [code=3.50.50.60, no name defined]                                                             3d8xA02 A:124-249  [code=3.50.50.60, no name defined]                                                                         3d8xA01 A:2-123,A:250-317  [code=3.50.50.60, no name defined]       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh....eee...hhhhh...hhhhhh.............hhhhhhhhhhhhhhhh..eee...eeeee.....eeeee........eeeeeeee...eee......hhhhhh...ee.hhhhhh.hhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhhh..eeee..eeeeeeee....eeeeeeee....eeeee...eeee...eee.hhhhh........................eee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------PYRIDINE_REDOX_2       ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d8x A   2 VHNKVTIIGSGPAAHTAAIYLARAEIKPILYEGMMANGIAAGGQLTTTTEIENFPGFPDGLTGSELMDRMREQSTKFGTEIITETVSKVDLSSKPFKLWTEFNEDAEPVTTDAIILATGASAKRMHLPGEETYWQKGISACAVCDGAVPIFRNKPLAVIGGGDSACEEAQFLTKYGSKVFMLVRKDHLRASTIMQKRAEKNEKIEILYNTVALEAKGDGKLLNALRIKNTKKNEETDLPVSGLFYAIGHTPATKIVAGQVDTDEAGYIKTVPGSSLTSVPGFFAAGDVQDSKYRQAITSAGSGCMAALDAEKYLTSLE 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with TRXB1_YEAST | P29509 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
          TRXB1_YEAST     2 VHNKVTIIGSGPAAHTAAIYLARAEIKPILYEGMMANGIAAGGQLTTTTEIENFPGFPDGLTGSELMDRMREQSTKFGTEIITETVSKVDLSSKPFKLWTEFNEDAEPVTTDAIILATGASAKRMHLPGEETYWQKGISACAVCDGAVPIFRNKPLAVIGGGDSACEEAQFLTKYGSKVFMLVRKDHLRASTIMQKRAEKNEKIEILYNTVALEAKGDGKLLNALRIKNTKKNEETDLPVSGLFYAIGHTPATKIVAGQVDTDEAGYIKTVPGSSLTSVPGFFAAGDVQDSKYRQAITSAGSGCMAALDAEKYLTSLE 319
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3d8xB01 B:2-123,B:250-317  [code=3.50.50.60, no name defined]                                                             3d8xB02 B:124-249  [code=3.50.50.60, no name defined]                                                                         3d8xB01 B:2-123,B:250-317  [code=3.50.50.60, no name defined]       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh....eee...hhhhh...hhhhhh.ee.........eehhhhhhhhhhhhhhh..eee...eeeee.....eeeee........eeeeeeee...eee......hhhhhh...ee.hhhhhh.hhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhhh..eeee..eeeeeeee....eeeeeeee....eeeeee..eeee...eee.hhhhh........................eee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------PYRIDINE_REDOX_2       ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d8x B   2 VHNKVTIIGSGPAAHTAAIYLARAEIKPILYEGMMANGIAAGGQLTTTTEIENFPGFPDGLTGSELMDRMREQSTKFGTEIITETVSKVDLSSKPFKLWTEFNEDAEPVTTDAIILATGASAKRMHLPGEETYWQKGISACAVCDGAVPIFRNKPLAVIGGGDSACEEAQFLTKYGSKVFMLVRKDHLRASTIMQKRAEKNEKIEILYNTVALEAKGDGKLLNALRIKNTKKNEETDLPVSGLFYAIGHTPATKIVAGQVDTDEAGYIKTVPGSSLTSVPGFFAAGDVQDSKYRQAITSAGSGCMAALDAEKYLTSLE 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

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 '\|'

(no "SCOP Domain" information available for 3D8X)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Saccharomyces cerevisiae. Organism_taxid: 4932. Strain: s288c. (1)

1a	3d8xA01	A:2-123,A:250-317
1b	3d8xB01	B:2-123,B:250-317
1c	3d8xA02	A:124-249
1d	3d8xB02	B:124-249

(no "Pfam Domain" information available for 3D8X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TRXB1_YEAST | P29509)

molecular function
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	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:0004791	thioredoxin-disulfide reductase activity	Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide.
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: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:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
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:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	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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Description

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Ligands, Modified Residues, Ions (2, 3)

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SS Bonds (2, 2)

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