1ZDL - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE THIOREDOXIN REDUCTASE TYPE 2

Authors :   E. I. Biterova, A. A. Turanov, V. N. Gladyshev, J. J. Barycki

Date :   14 Apr 05 (Deposition) - 01 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

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

Reference :   E. I. Biterova, A. A. Turanov, V. N. Gladyshev, J. J. Barycki
Crystal Structures Of Oxidized And Reduced Mitochondrial Thioredoxin Reductase Provide Molecular Details Of The Reaction Mechanism.
Proc. Natl. Acad. Sci. Usa V. 102 15018 2005
PubMed-ID: 16217027 | Reference-DOI: 10.1073/PNAS.0504218102
(for further references see the PDB file header)

Molecule 1 - THIOREDOXIN REDUCTASE 2, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	1.8.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TXNRD2, TRXR2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	TR3

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

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

Biological Unit 1 (2, 4)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:46 , SER A:49 , GLY A:50 , ASP A:69 , TYR A:70 , GLY A:84 , THR A:85 , CYS A:86 , GLY A:90 , CYS A:91 , LYS A:94 , LYS A:158 , ALA A:159 , ALA A:187 , THR A:188 , GLY A:189 , ARG A:318 , GLU A:321 , LEU A:325 , ILE A:357 , GLY A:358 , ASP A:359 , GLU A:366 , LEU A:367 , THR A:368 , PRO A:369 , PHE A:400 , HIS A:497 , PRO A:498 , NDP A:700	BINDING SITE FOR RESIDUE FAD A 600
2	AC2	SOFTWARE	LYS A:94 , ALA A:226 , SER A:227 , TYR A:228 , VAL A:229 , GLU A:232 , ARG A:249 , SER A:250 , ARG A:254 , ALA A:315 , ILE A:316 , GLY A:317 , GLU A:366 , LEU A:367 , THR A:397 , THR A:398 , FAD A:600	BINDING SITE FOR RESIDUE NDP A 700

Asymmetric Unit

No.	Residues
1	A:483	-	A:483

Asymmetric Unit

No.	Residues
1	Gln A:119	-	Pro A:120
2	Pro A:456	-	Pro A:457
3	His A:497	-	Pro A:498

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_1	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.	TRXR2_MOUSE	83-93	1	A:83-93

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_1	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.	TRXR2_MOUSE	83-93	2	A:83-93

(no "Exon" information available for 1ZDL)

Asymmetric 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:484
 aligned with TRXR2_MOUSE | Q9JLT4 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:484
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517    
          TRXR2_MOUSE    38 QSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTG 521
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zdlA01 A:38-192,A:317-393  [code=3.50.50.60, no name defined]                                                                                             1zdlA02 A:193-316  [code=3.50.50.60, no name defined]                                                                       1zdlA01 A:38-192,A:317-393  [code=3.50.50.60, no name defined]               1zdlA03 A:394-521  [code=3.30.390.30, no name defined]                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.hhhhhhhhhhh...ee....eee....eeee.........ee...eee...eee.......hhhhhh.hhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhh...ee...eeeeeeee.....eeeeeee......eeeee.eeee...eee.hhhhhhhhh.......................eee...........hhhhhhhhhhhhhhhhh............eee....eeeeee.hhhhhhhhhh...eeeeeee..hhhhhhh.......eeeeeee......eeeeeeee.hhhhhhhhhhhhhhhh.hhhhhhh.......hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------PYRIDINE_RE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zdl A  38 QSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTG 521
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517

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 1ZDL)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

House mouse (Mus musculus) (2)

1zdlA03

A:394-521

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

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

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

House mouse (Mus musculus) (2)

2a	1zdlA01	A:38-192,A:317-393
2b	1zdlA02	A:193-316

(no "Pfam Domain" information available for 1ZDL)

Asymmetric Unit(hide GO term definitions)

Chain A (TRXR2_MOUSE | Q9JLT4)

molecular function
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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:0016668	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	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:0000305	response to oxygen radical	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 an oxygen radical stimulus. An oxygen radical is any oxygen species that carries a free electron; examples include hydroxyl radicals and the superoxide anion.
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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:119 - Pro A:120	[ RasMol ]
		His A:497 - Pro A:498	[ RasMol ]
		Pro A:456 - Pro A:457	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1zdl
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TRXR2_MOUSE \| Q9JLT4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.8.1.9
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TRXR2_MOUSE \| Q9JLT4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TRXR2_MOUSE \| Q9JLT4	:	1zkq 3dgz

1h6v	MAMMALIAN THIOREDOXIN REDUCTASE (RAT TYPE I)
3grs	REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 A RESOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File