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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN GLUTAREDOXIN 5 WITH BOUND GLUTATHIONE IN AN FES CLUSTER

Authors :   A. K. Roos, C. Johansson, K. Guo, W. W. Yue, A. C. W. Pike, C. D. O. Cooper, E K. L. Kavanagh, A. Chaikuad, F. Von Delft, C. H. Arrowsmith, J. Weigel A. Edwards, C. Bountra, U. Oppermann

Date :   06 Oct 09 (Deposition) - 20 Oct 09 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Chromosome 14 Open Reading Frame 87, Oxidoreductase, Thioredoxin Family, Glrx5, Pr01238, Flb4739 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Johansson, A. K. Roos, S. J. Montano, R. Sengupta, P. Filippakopoulos, K. Guo, F. Von Delft, A. Holmgren, U. Oppermann, K. L. Kavanagh
The Crystal Structure Of Human Glrx5: Iron Sulphur Cluster Coordination, Tetrameric Assembly And Monomer Activity.
Biochem. J. V. 433 303 2011
PubMed-ID: 21029046 | Reference-DOI: 10.1042/BJ20101286

Molecule 1 - GLUTAREDOXIN RELATED PROTEIN 5
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Fragment	:	RESIDUES 35-150
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	GSH	4	Ligand/Ion	GLUTATHIONE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:59 , PHE A:69 , ARG A:97 , LYS A:101 , THR A:108 , ILE A:109 , GLY A:121 , CYS A:122 , ASP A:123 , FES A:1150 , HOH A:2008 , HOH A:2010 , HOH A:2013 , HOH D:2030 , HOH D:2032	BINDING SITE FOR RESIDUE GSH A 300
02	AC2	SOFTWARE	CYS A:67 , PHE A:69 , GSH A:300 , LYS B:59 , CYS B:67 , PHE B:69 , GSH B:300	BINDING SITE FOR RESIDUE FES A1150
03	AC3	SOFTWARE	FES A:1150 , LYS B:59 , PHE B:69 , ARG B:97 , LYS B:101 , THR B:108 , ILE B:109 , GLY B:121 , CYS B:122 , ASP B:123 , HOH B:2019 , HOH B:2022 , HOH B:2027 , HOH B:2028 , HOH B:2029	BINDING SITE FOR RESIDUE GSH B 300
04	AC4	SOFTWARE	ARG A:97 , PRO B:65 , CYS B:67	BINDING SITE FOR RESIDUE CL B1150
05	AC5	SOFTWARE	VAL C:119	BINDING SITE FOR RESIDUE PEG B1151
06	AC6	SOFTWARE	HOH B:2028 , LYS C:59 , PHE C:69 , ARG C:97 , LYS C:101 , THR C:108 , ILE C:109 , PRO C:110 , GLY C:121 , CYS C:122 , ASP C:123 , FES C:1149 , HOH C:2015 , HOH C:2016 , HOH C:2017	BINDING SITE FOR RESIDUE GSH C 300
07	AC7	SOFTWARE	CYS C:67 , GSH C:300 , LYS D:59 , CYS D:67 , PHE D:69 , GSH D:300	BINDING SITE FOR RESIDUE FES C1149
08	AC8	SOFTWARE	HOH A:2013 , FES C:1149 , LYS D:59 , PHE D:69 , ARG D:97 , LYS D:101 , THR D:108 , ILE D:109 , GLY D:121 , CYS D:122 , ASP D:123 , HOH D:2023 , HOH D:2029 , HOH D:2030 , HOH D:2031 , HOH D:2032 , HOH D:2033	BINDING SITE FOR RESIDUE GSH D 300
09	AC9	SOFTWARE	ARG C:97 , CYS D:67	BINDING SITE FOR RESIDUE CL D1150
10	BC1	SOFTWARE	LYS D:53 , ASP D:84	BINDING SITE FOR RESIDUE CL D1151
11	BC2	SOFTWARE	GLU B:117 , LYS D:50	BINDING SITE FOR RESIDUE CL D1152

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

Asymmetric/Biological Unit

No.	Residues
1	Ile A:109	-	Pro A:110
2	Ile B:109	-	Pro B:110
3	Ile C:109	-	Pro C:110
4	Ile D:109	-	Pro D:110

Asymmetric/Biological Unit (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074550	K	101	Q	GLRX5_HUMAN	Disease (SIDBA3)	869312752	A/B/C/D	K	101	Q
2	UniProt	VAR_026125	A	146	T	GLRX5_HUMAN	Polymorphism	11628901	A/B/C/D	A	146	T
3	UniProt	VAR_074551	L	148	S	GLRX5_HUMAN	Disease (SIDBA3)	765487627	A/B/C/D	L	148	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	GLRX5_HUMAN	42-145	4	A:42-145 B:42-145 C:42-145 D:42-145

(no "Exon" information available for 2WUL)

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:109
 aligned with GLRX5_HUMAN | Q86SX6 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    50        60        70        80        90       100       110       120       130       140         
          GLRX5_HUMAN    41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh.....eeee...hhhhhh.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------Q--------------------------------------------T-S- SAPs(SNPs)
                    PROSITE -GLUTAREDOXIN_2  PDB: A:42-145 UniProt: 42-145                                                           ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wul A  41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
                                    50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with GLRX5_HUMAN | Q86SX6 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    50        60        70        80        90       100       110       120       130       140         
          GLRX5_HUMAN    41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeee..........hhhhhhhhhhhh.....eeee...hhhhhh.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------Q--------------------------------------------T-S- SAPs(SNPs)
                    PROSITE -GLUTAREDOXIN_2  PDB: B:42-145 UniProt: 42-145                                                           ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wul B  41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
                                    50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:109
 aligned with GLRX5_HUMAN | Q86SX6 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    49        59        69        79        89        99       109       119       129       139         
          GLRX5_HUMAN    40 GSAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALL 148
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh.....eeee...hhhhhh.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------Q--------------------------------------------T-S SAPs(SNPs)
                    PROSITE --GLUTAREDOXIN_2  PDB: C:42-145 UniProt: 42-145                                                           --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wul C  40 GSAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALL 148
                                    49        59        69        79        89        99       109       119       129       139

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with GLRX5_HUMAN | Q86SX6 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    50        60        70        80        90       100       110       120       130       140         
          GLRX5_HUMAN    41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Glutaredoxin-2wulD01 D:54-119                                     ------------------------------ Pfam domains (1)
           Pfam domains (2) -------------Glutaredoxin-2wulD02 D:54-119                                     ------------------------------ Pfam domains (2)
           Pfam domains (3) -------------Glutaredoxin-2wulD03 D:54-119                                     ------------------------------ Pfam domains (3)
           Pfam domains (4) -------------Glutaredoxin-2wulD04 D:54-119                                     ------------------------------ Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh.....eeee...hhhhhh.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------Q--------------------------------------------T-S- SAPs(SNPs)
                    PROSITE -GLUTAREDOXIN_2  PDB: D:42-145 UniProt: 42-145                                                           ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2wul D  41 SAEQLDALVKKDKVVVFLKGTPEQPQCGFSNAVVQILRLHGVRDYAAYNVLDDPELRQGIKDYSNWPTIPQVYLNGEFVGGCDILLQMHQNGDLVEELKKLGIHSALLD 149
                                    50        60        70        80        90       100       110       120       130       140

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 2WUL)

(no "CATH Domain" information available for 2WUL)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Glutaredoxin (22)

Homo sapiens (Human) (2)

1a	Glutaredoxin-2wulD01	D:54-119
1b	Glutaredoxin-2wulD02	D:54-119
1c	Glutaredoxin-2wulD03	D:54-119
1d	Glutaredoxin-2wulD04	D:54-119

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (GLRX5_HUMAN | Q86SX6)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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.
cellular component
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	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: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.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Ile C:109 - Pro C:110	[ RasMol ]
		Ile D:109 - Pro D:110	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

PROSITE Motifs (1, 4)

Exons (0, 0)

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