1M0T - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   YEAST GLUTATHIONE SYNTHASE

Authors :   A. Gogos, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   14 Jun 02 (Deposition) - 11 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Amine/Carboxylate Ligase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Gogos, L. Shapiro
Large Conformational Changes In The Catalytic Cycle Of Glutathione Synthase
Structure V. 10 1669 2002
PubMed-ID: 12467574 | Reference-DOI: 10.1016/S0969-2126(02)00906-1
(for further references see the PDB file header)

Molecule 1 - GLUTATHIONE SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.3.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET28TEV
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	GSH2
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GLUTATHIONE SYNTHASE, GSH SYNTHETASE, GSH-S

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 4)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:74 , SER A:341 , ASP A:342 , LYS A:345 , GLN B:1210	BINDING SITE FOR RESIDUE SO4 B 501
2	AC2	SOFTWARE	GLN A:210 , ARG B:1074 , ILE B:1340 , SER B:1341 , ASP B:1342 , LYS B:1345	BINDING SITE FOR RESIDUE SO4 B 502
3	AC3	SOFTWARE	ARG B:1128 , PHE B:1154 , ARG B:1467 , HOH B:2116 , HOH B:2349	BINDING SITE FOR RESIDUE SO4 B 503
4	AC4	SOFTWARE	ARG A:128 , SER A:153 , ARG A:467	BINDING SITE FOR RESIDUE SO4 A 504
5	AC5	SOFTWARE	LEU A:112 , SER A:114 , ALA A:115 , LYS A:119 , ARG A:366	BINDING SITE FOR RESIDUE SO4 A 505
6	AC6	SOFTWARE	ASN A:25 , LYS A:160 , THR B:1024 , ASN B:1025 , HOH B:2439	BINDING SITE FOR RESIDUE SO4 B 506

(no "SS Bond" information available for 1M0T)

Asymmetric Unit

No.	Residues
1	Ala A:313	-	Pro A:314
2	Ala B:1313	-	Pro B:1314

(no "SAP(SNP)/Variant" information available for 1M0T)

(no "PROSITE Motif" information available for 1M0T)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOL049W	1	YOL049W.1	XV:238618-240093	1476	GSHB_YEAST	1-491	491	2	A:5-491 (gaps) B:1005-1491 (gaps)	487 487

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:454
 aligned with GSHB_YEAST | Q08220 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:487
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          GSHB_YEAST      5 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY  491
               SCOP domains d1m0ta2 A:5-213,A:324-491 Eukaryotic glutathione synthetase ATP-binding domain                                                                                                                                   d1m0ta1 A:214-323 Eukaryotic glutathione synthetase, substrate-binding domain                                 d1m0ta2 A:5-213,A:324-491 Eukaryotic glutathione synthetase A    TP-binding domain                                                                                       SCOP domains
               CATH domains --1m0tA01 A:7-51,A:160-188,A:427-437           1m0tA02     1m0tA03 A:64-115,A:323-             355             --1m0tA02 A:52-63,A:1   18-159,A:438-491    1m0tA01                      1m0tA04 A:189-322  [code=3.40.50.1760, no name defined]                                                                               1m0tA03 A:64-115,A:323-355       1m0tA05 A:356-417  [code=3.30    .1490.50, no name defined]   ---------1m0tA01    1m0tA02 A:52-63,A:118-159,A:438-             491       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..ee...hhhhh..eeee..ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh......-------------hhhhhhhhhhhhh..........eeeeeeeeeeee..---.eeeeeeee.....hhhhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhheee......eee.....eeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhh.hhhhhhhh.hhhhhhh...hhhhhhhhhhhh..eee...hhhhhhhhhhhhhh...eeeee.----...ee..hhhhhhhhhhhhhhh.eeeee...........eee..eee....eeeeeeeeeeee....eeeeeeeeeeeeee-------------.ee..eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-491 (gaps) UniProt: 1-491 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                1m0t A    5 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYL-------------FTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKK---EQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQ----GNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSK-------------GCLDSIILY  491
                                    14        24        34        44        54        64        74        84 |       -     | 104       114       124       134 |   | 144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384    |  394       404       414       424       434       444       454       464    |    -       484       
                                                                                                            86           100                                 136 140                                                                                                                                                                                                                                                 384  389                                                                             469           483

Chain B from PDB  Type:PROTEIN  Length:455
 aligned with GSHB_YEAST | Q08220 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:487
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          GSHB_YEAST      5 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY  491
               SCOP domains d1m0tb2 B:1005-1213,B:1324-1491 Eukaryotic glutathione synthetase ATP-binding doma            in                                                                                                                 d1m0tb1 B:1214-1323 Eukaryotic glutathione synthetase, substrate-binding domain                               d1m0tb2 B:1005-1213,B:1324-1491 Eukaryotic glutathione synthe     tase ATP-binding domain                                                                                SCOP domains
               CATH domains --1m0tB01 B:1007-1051,B:1160-1188,B:1427-1437  1m0tB02     1m0tB03 B:1064-1114,B:1            323-1355        --1m0tB02 B:1052-1063,   B:1117-1159,B:1438-11m0tB01                      1m0tB04 B:1189-1322  [code=3.40.50.1760, no name defined]                                                                             1m0tB03 B:1064-1114,B:1323-1355  1m0tB05 B:1356-1417  [code=3.     30.1490.50, no name defined]---------1m0tB01    1m0tB02 B:1052-1063,B:1117-1159,B            :1438-149 CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-1m0tB01 B:1216-1321                                                                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-1m0tB02 B:1216-1321                                                                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) GSH_synth_ATP-1m0tB03 B:1005-1490                                                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (3)
           Pfam domains (4) GSH_synth_ATP-1m0tB04 B:1005-1490                                                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..ee...hhhhh..eeee..ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh......------------hhhhhhhhhhhhhh..........eeeeeeeeeeee..---.eeeeeeee.....hhhhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhheee......eee.....eeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhh...eee...hhhhhhhhhhhhhh...eeee..-----..ee..hhhhhhhh.hhhhhh..eeee...........eee..eee....eeeeeeeeeeee....eeeeeeeeeeeeee.------------.eee.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1005-1491 (gaps) UniProt: 1-491 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                1m0t B 1005 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYL------------EFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKK---EQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQ-----NNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKF------------GCLDSIILY 1491
                                  1014      1024      1034      1044      1054      1064      1074      1084 |       -    | 1104      1114      1124      1134 |   |1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384     |1394      1404      1414      1424      1434      1444      1454      1464     |   -      1484       
                                                                                                          1086         1099                                 1136   |                                                                                                                                                                                                                                                1384  1390                                                                            1470         1483        
                                                                                                                                                                1140

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(hide GO term definitions)

Chain A,B (GSHB_YEAST | Q08220)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0043295	glutathione binding	Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine.
	GO:0004363	glutathione synthase activity	Catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H(+) + phosphate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006750	glutathione biosynthetic process	The chemical reactions and pathways resulting in the formation of 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.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:313 - Pro A:314	[ RasMol ]
		Ala B:1313 - Pro B:1314	[ RasMol ]

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	1m0t
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	GSHB_YEAST \| Q08220	:	1m0w

1m0w	1M0W IS YEAST GLUTATHIONE SYNTHASE BOUND TO GAMMA-GLUTAMYL- CYSTEINE, AMP-PNP AND 2 MAGNESIUM IONS RELATED ID: NYSGXRC-P102 RELATED DB: TARGETDB
2hgs	2HGS IS HUMAN GLUTATHIONE SYNTHETASE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

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