3DJG - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CATALYTIC CYCLE OF HUMAN GLUTATHIONE REDUCTASE NEAR 1 A RESOLUTION

Authors :   D. S. Berkholz, H. R. Faber, S. N. Savvides, P. A. Karplus

Date :   23 Jun 08 (Deposition) - 05 Aug 08 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Flavoenzyme, Glutathione, Nicotinamide, Alternative Initiation, Fad, Flavoprotein, Mitochondrion, Nadp, Oxidoreductase, Phosphoprotein, Redox-Active Center, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Berkholz, H. R. Faber, S. N. Savvides, P. A. Karplus
Catalytic Cycle Of Human Glutathione Reductase Near 1 A Resolution.
J. Mol. Biol. V. 382 371 2008
PubMed-ID: 18638483 | Reference-DOI: 10.1016/J.JMB.2008.06.083

Molecule 1 - GLUTATHIONE REDUCTASE
	Chains	:	X
	EC Number	:	1.8.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 45 TO 522
	Gene	:	GSR, GLUR, GRD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GRASE, GR

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

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 X:27 , GLY X:29 , SER X:30 , GLY X:31 , GLU X:50 , SER X:51 , HIS X:52 , GLY X:56 , THR X:57 , CYS X:58 , GLY X:62 , CYS X:63 , LYS X:66 , GLY X:128 , HIS X:129 , ALA X:130 , ALA X:155 , THR X:156 , GLY X:157 , ARG X:291 , LEU X:298 , GLY X:330 , ASP X:331 , LEU X:337 , LEU X:338 , THR X:339 , PRO X:340 , HIS X:467 , PRO X:468 , HOH X:485 , HOH X:487 , HOH X:493 , HOH X:498 , HOH X:534 , HOH X:795 , HOH X:827 , HOH X:832	BINDING SITE FOR RESIDUE FAD X 479
2	AC2	SOFTWARE	LYS X:66 , ALA X:195 , GLY X:196 , TYR X:197 , ILE X:198 , GLU X:201 , ARG X:218 , HIS X:219 , ARG X:224 , ILE X:289 , GLY X:290 , ARG X:291 , LEU X:337 , LEU X:338 , PHE X:372 , HOH X:507 , HOH X:510 , HOH X:520 , HOH X:535 , HOH X:568 , HOH X:592 , HOH X:797 , HOH X:839 , HOH X:840 , HOH X:853 , HOH X:939 , HOH X:990 , HOH X:998	BINDING SITE FOR RESIDUE NDP X 483

Asymmetric Unit

No.	Residues
1	X:90	-	X:90

Asymmetric Unit

No.	Residues
1	His X:374	-	Pro X:375
2	His X:467	-	Pro X:468

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019079	R	153	C	GSHR_HUMAN	Polymorphism	8190955	X	R	109	C
2	UniProt	VAR_051775	G	232	R	GSHR_HUMAN	Polymorphism	8190976	X	G	188	R
3	UniProt	VAR_019080	G	232	S	GSHR_HUMAN	Polymorphism	8190976	X	G	188	S
4	UniProt	VAR_019081	I	261	V	GSHR_HUMAN	Polymorphism	8190997	X	I	217	V
5	UniProt	VAR_019082	E	297	D	GSHR_HUMAN	Polymorphism	8191004	X	E	253	D
6	UniProt	VAR_014554	P	314	H	GSHR_HUMAN	Polymorphism	2020916	X	P	270	H

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

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019079	R	153	C	GSHR_HUMAN	Polymorphism	8190955	X	R	109	C
2	UniProt	VAR_051775	G	232	R	GSHR_HUMAN	Polymorphism	8190976	X	G	188	R
3	UniProt	VAR_019080	G	232	S	GSHR_HUMAN	Polymorphism	8190976	X	G	188	S
4	UniProt	VAR_019081	I	261	V	GSHR_HUMAN	Polymorphism	8190997	X	I	217	V
5	UniProt	VAR_019082	E	297	D	GSHR_HUMAN	Polymorphism	8191004	X	E	253	D
6	UniProt	VAR_014554	P	314	H	GSHR_HUMAN	Polymorphism	2020916	X	P	270	H

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

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.	GSHR_HUMAN	99-109	1	X:55-65

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.	GSHR_HUMAN	99-109	2	X:55-65

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000221130	1a	ENSE00001167123	chr8:30585443-30585047	397	GSHR_HUMAN	1-102	102	1	X:18-58	41
1.3	ENST00000221130	3	ENSE00001158437	chr8:30569605-30569579	27	GSHR_HUMAN	103-111	9	1	X:59-67	9
1.4	ENST00000221130	4	ENSE00001158427	chr8:30567419-30567331	89	GSHR_HUMAN	112-141	30	1	X:68-97	30
1.5	ENST00000221130	5	ENSE00001158417	chr8:30565658-30565589	70	GSHR_HUMAN	141-164	24	1	X:97-120	24
1.6	ENST00000221130	6	ENSE00001158408	chr8:30560757-30560610	148	GSHR_HUMAN	165-214	50	1	X:121-170	50
1.7	ENST00000221130	7	ENSE00000687921	chr8:30557652-30557598	55	GSHR_HUMAN	214-232	19	1	X:170-188	19
1.8b	ENST00000221130	8b	ENSE00000687915	chr8:30553996-30553897	100	GSHR_HUMAN	232-265	34	1	X:188-221	34
1.9	ENST00000221130	9	ENSE00000687910	chr8:30550572-30550486	87	GSHR_HUMAN	266-294	29	1	X:222-250	29
1.10b	ENST00000221130	10b	ENSE00000687906	chr8:30546836-30546678	159	GSHR_HUMAN	295-347	53	1	X:251-303	53
1.11	ENST00000221130	11	ENSE00000687902	chr8:30541716-30541605	112	GSHR_HUMAN	348-385	38	1	X:304-341	38
1.12b	ENST00000221130	12b	ENSE00000687899	chr8:30539578-30539447	132	GSHR_HUMAN	385-429	45	1	X:341-385	45
1.13	ENST00000221130	13	ENSE00000687897	chr8:30538554-30538421	134	GSHR_HUMAN	429-473	45	1	X:385-429	45
1.14b	ENST00000221130	14b	ENSE00002132314	chr8:30537186-30535583	1604	GSHR_HUMAN	474-522	49	1	X:430-478	49

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 X from PDB  Type:PROTEIN  Length:461
 aligned with GSHR_HUMAN | P00390 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:461
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521 
           GSHR_HUMAN    62 VASYDYLVIGGGSGGLASARRAAELGARAAVVESHKLGGTCVNVGCVPKKVMWNTAVHSEFMHDHADYGFPSCEGKFNWRVIKEKRDAYVSRLNAIYQNNLTKSHIEIIRGHAAFTSDPKPTIEVSGKKYTAPHILIATGGMPSTPHESQIPGASLGITSDGFFQLEELPGRSVIVGAGYIAVEMAGILSALGSKTSLMIRHDKVLRSFDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVTAVPGRLPVMTMIPDVDCLLWAIGRVPNTKDLSLNKLGIQTDDKGHIIVDEFQNTNVKGIYAVGDVCGKALLTPVAIAAGRKLAHRLFEYKEDSKLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR 522
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eee......eeee..eeee...eee...eee.........hhhhh.hhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eee..eeeeeeeee..eeeeeeee.......eeeeeeee.eeee...eee.hhhhhhhhh......................eee.hhhhh...hhhhhhhhhhhhhhhhhh.............eee.....eeeee.hhhhhhhhhh...eeeeeeee.hhhhhhh.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------C------------------------------------------------------------------------------R----------------------------V-----------------------------------D----------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------PYRIDINE_RE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: X:18-58 UniProt: 1-102   Exon 1.3 Exon 1.4  PDB: X:68-97        -----------------------Exon 1.6  PDB: X:121-170 UniProt: 165-214         -----------------Exon 1.8b  PDB: X:188-221         Exon 1.9  PDB: X:222-250     Exon 1.10b  PDB: X:251-303 UniProt: 295-347          Exon 1.11  PDB: X:304-341             -------------------------------------------Exon 1.13  PDB: X:385-429 UniProt: 429-473   Exon 1.14b  PDB: X:430-478 UniProt: 474-522       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.5  PDB: X:97-120 -------------------------------------------------Exon 1.7           --------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12b  PDB: X:341-385 UniProt: 385-429  --------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3djg X  18 VASYDYLVIGGGSGGLASARRAAELGARAAVVESHKLGGTCVNVGCVPKKVMWNTAVHSEFMHDHADYGFPSCEGKFNWRVIKEKRDAYVSRLNAIYQNNLTKSHIEIIRGHAAFTSDPKPTIEVSGKKYTAPHILIATGGMPSTPHESQIPGASLGITSDGFFQLEELPGRSVIVGAGYIAVEMAGILSALGSKTSLMIRHDKVLRSFDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVTAVPGRLPVMTMIPDVDCLLWAIGRVPNTKDLSLNKLGIQTDDKGHIIVDEFQNTNVKGIYAVGDVCGKALLTPVAIAAGRKLAHRLFEYKEDSKLDYNNIPTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIHPTSSEELVTLR 478
                                    27        37        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

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 3DJG)

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

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

Asymmetric Unit(hide GO term definitions)

Chain X (GSHR_HUMAN | P00390)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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: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:0004362	glutathione-disulfide reductase activity	Catalysis of the reaction: 2 glutathione + NADP+ = glutathione disulfide + NADPH + H+.
	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.
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:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	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:0000302	response to reactive oxygen species	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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
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:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		His X:374 - Pro X:375	[ RasMol ]
		His X:467 - Pro X:468	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3djg
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	GSHR_HUMAN \| P00390
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	1.8.1.7
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3djj	THE SAME PROTEIN-LIGAND COMPLEX AT HIGHER RESOLUTION AND CRYOTEMPERATURE INSTEAD OF ROOM TEMPERATURE.
3dk4
3dk8
3dk9

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

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Exons (13, 13)

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