3UIW - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   ZEBRAFISH GRX2 (APO)

Authors :   M. A. Mcdonough, C. Johansson

Date :   06 Nov 11 (Deposition) - 27 Mar 13 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)

Keywords :   Thioredoxin/Glutaredoxin Fold, Oxidoreductase, Glutathione, 2Fe2S Cluster (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Brautigam, C. Johansson, B. Kubsch, M. A. Mcdonough, E. Bill, A. Holmgren, C. Berndt
A New Mode Of Iron-Sulfur Cluster Coordination In Glutaredoxins Is Crucial For Axonogenesis
To Be Published
PubMed: search

Molecule 1 - GLUTAREDOXIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GSH	2	Ligand/Ion	GLUTATHIONE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GSH	1	Ligand/Ion	GLUTATHIONE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GSH	1	Ligand/Ion	GLUTATHIONE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	GSH	4	Ligand/Ion	GLUTATHIONE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:34 , CYS A:37 , PRO A:38 , TYR A:39 , GLN A:69 , THR A:80 , VAL A:81 , PRO A:82 , GLY A:93 , GLY A:94 , SER A:95 , HOH A:301 , HOH A:304 , HOH A:323	BINDING SITE FOR RESIDUE GSH A 201
2	AC2	SOFTWARE	SER A:26 , CYS A:28 , CYS A:116 , CYS A:117 , HOH A:333 , HOH A:334	BINDING SITE FOR RESIDUE SO4 A 202
3	AC3	SOFTWARE	LYS B:34 , CYS B:37 , PRO B:38 , TYR B:39 , GLN B:69 , THR B:80 , VAL B:81 , GLY B:94 , SER B:95 , ASP B:96	BINDING SITE FOR RESIDUE GSH B 201

Asymmetric Unit

No.	Residues
1	A:28	-	A:113
2	A:116	-	A:116
3	B:28	-	B:113
4	B:116	-	B:116

Asymmetric Unit

No.	Residues
1	Val A:81	-	Pro A:82
2	Val B:81	-	Pro B:82

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

(no "PROSITE Motif" information available for 3UIW)

(no "Exon" information available for 3UIW)

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:110
 aligned with Q6DH06_DANRE | Q6DH06 from UniProtKB/TrEMBL  Length:134

    Alignment length:110
                                    18        28        38        48        58        68        78        88        98       108       118
         Q6DH06_DANRE     9 PGLSSSACGQFVQDIVSSNCVVIFSKTTCPYCKMAKGVFNEIGATYKVVELDEHNDGRRLQETLAELTGARTVPRVFINGQCIGGGSDTKQLHQQGKLLPLIEQCRPCCL 118
               SCOP domains d3uiwa_ A: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3uiw A   9 PGLSSSACGQFVQDIVSSNCVVIFSKTTCPYCKMAKGVFNEIGATYKVVELDEHNDGRRLQETLAELTGARTVPRVFINGQCIGGGSDTKQLHQQGKLLPLIEQCRPCCL 118
                                    18        28        38        48        58        68        78        88        98       108       118

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with Q6DH06_DANRE | Q6DH06 from UniProtKB/TrEMBL  Length:134

    Alignment length:109
                                    19        29        39        49        59        69        79        89        99       109         
         Q6DH06_DANRE    10 GLSSSACGQFVQDIVSSNCVVIFSKTTCPYCKMAKGVFNEIGATYKVVELDEHNDGRRLQETLAELTGARTVPRVFINGQCIGGGSDTKQLHQQGKLLPLIEQCRPCCL 118
               SCOP domains d3uiwb_ B: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3uiw B  10 GLSSSACGQFVQDIVSSNCVVIFSKTTCPYCKMAKGVFNEIGATYKVVELDEHNDGRRLQETLAELTGARTVPRVFINGQCIGGGSDTKQLHQQGKLLPLIEQCRPCCL 118
                                    19        29        39        49        59        69        79        89        99       109

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 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)

Zebrafish (Danio rerio) [TaxId: 7955] (1)

1a	d3uiwa_	A:
1b	d3uiwb_	B:

(no "CATH Domain" information available for 3UIW)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q6DH06_DANRE | Q6DH06)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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: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:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0060914	heart formation	The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.
	GO:0001755	neural crest cell migration	The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
	GO:0003147	neural crest cell migration involved in heart formation	The characteristic movement of a cell from the dorsal ridge of the neural tube towards the heart and that contributes to heart formation.
	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:0080058	protein deglutathionylation	The protein modification process in which a glutathione molecule is removed from a protein amino acid by breaking a disulfide linkage.
	GO:0001944	vasculature development	The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
		Val A:81 - Pro A:82	[ RasMol ]
		Val B:81 - Pro B:82	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 3)

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SS Bonds (4, 4)

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