3KAK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN OPEN CONFORMATION WITH GAMMA-GLUTAMYL-CYSTEINE BOUND.

Authors :   A. Galant, K. A. J. Arkus, C. Zubieta, R. E. Cahoon, J. M. Jez

Date :   19 Oct 09 (Deposition) - 22 Dec 09 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

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

Keywords :   Dimer, Atp-Grasp Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Galant, K. A. Arkus, C. Zubieta, R. E. Cahoon, J. M. Jez
Structural Basis For Evolution Of Product Diversity In Soybean Glutathione Biosynthesis.
Plant Cell V. 21 3450 2009
PubMed-ID: 19948790 | Reference-DOI: 10.1105/TPC.109.071183
(for further references see the PDB file header)

Molecule 1 - HOMOGLUTATHIONE SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.3.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS8
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HGS
	Organism Common	:	SOYBEANS
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	3GC	3	Ligand/Ion	GAMMA-GLUTAMYLCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:153 , ILE A:173 , SER A:174 , THR A:175 , SER A:176 , GLN A:238 , GLU A:241 , ASN A:243 , ARG A:295 , TYR A:298	BINDING SITE FOR RESIDUE 3GC A 501
2	AC2	SOFTWARE	ARG B:153 , SER B:174 , SER B:176 , GLN B:238 , GLU B:241 , ASN B:243 , ARG B:295 , TYR B:298	BINDING SITE FOR RESIDUE 3GC B 501
3	AC3	SOFTWARE	TRP B:90 , LYS B:91 , CYS B:94 , PRO B:207 , ALA B:208 , GLU B:469	BINDING SITE FOR RESIDUE 3GC B 502

(no "SS Bond" information available for 3KAK)

Asymmetric/Biological Unit

No.	Residues
1	Cys A:323	-	Pro A:324
2	Cys B:323	-	Pro B:324

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

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

(no "Exon" information available for 3KAK)

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:443
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:473
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496   
         Q9M426_SOYBN    27 PLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------3kakA02     3kakA03 A:96-142,A:333-36    5                 3  kakA02 A:84-95,A:143-182,A:443-498   --------------------------3kakA04 A:209-332  [code=3.40.50.1760, no name defined]                                                                     3kakA03 A:96-142,A:333-365       -------------------------     --------------         ------------------------3kakA02 A:84-95,A:143-182,A:443-498                     - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh..eee..............eee..ee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----hhhhhhhhhhhhhhhh...--.eeeeeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhh....eeeeehhhhhhhhee.....eee..eeeeeeee....hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh..ee..hhhhhhhhhhh.....eee..-----..eehhhhh.....---------...eee.......eeeeeee..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.----------..eee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kak A  27 PLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSR----DEFTSRLLDIHSKMLQINK--DIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQ-----NNIYGDELRETLLK---------AAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKIS----------FGVVDTVYLT 499
                                    36        46        56        66        76        86        96       106       116   |   126       136      |146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386   |   396       406  |      -  |    426       436       446       456       466       476  |      -   |   496   
                                                                                                                       120  125               143  |                                                                                                                                                                                                                                                 390   396          409       419                                                         479        490         
                                                                                                                                                 146

Chain B from PDB  Type:PROTEIN  Length:437
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:470
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499
         Q9M426_SOYBN    30 DYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------3kakB02     3kakB03 B:96-142,B:333-36   5                  3kakB02 B:84-95,B:143-182,B:443-498     --------------------------3kakB04 B:209-332  [code=3.40.50.1760, no name defined]                                                                     3kakB03 B:96-142,B:333-365       -------------------------                              ----------------------3kakB02 B:84-95,B:143-182,B:443-498                     - CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kakB01 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kakB02 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) GSH_synth_ATP-3kakB03 B:30-498                                                                                                                                                                                                                                                                                                                                                                                                                                                       - Pfam domains (3)
           Pfam domains (4) GSH_synth_ATP-3kakB04 B:30-498                                                                                                                                                                                                                                                                                                                                                                                                                                                       - Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..eee............eeeee..ee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh....eeeehhhhhhhheee.....eee..eeeeeeee....hhhhh..hhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhh..ee.......hhhhhh..........------------------------------..ee.......eeeeeee..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee..............eee.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kak B  30 DYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSR---ADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQ------------------------------YILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
                                    39        49        59        69        79        89        99       109       119|   |  129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389|        -         -         - |     429       439       449       459       469       479       489       499
                                                                                                                    120 124                                                                                                                                                                                                                                                                       390                            421

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 3KAK)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: ATP-grasp fold, B domain (118)

Soybeans (Glycine max) (2)

1a	3kakB02	B:84-95,B:143-182,B:443-498
1b	3kakA02	A:84-95,A:143-182,A:443-498

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1760, no name defined] (6)

Soybeans (Glycine max) (2)

2a	3kakA04	A:209-332
2b	3kakB04	B:209-332

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Glutathione Synthetase; Chain A, domain 3 (6)

Homologous Superfamily: Glutathione Synthetase; Chain A, domain 3 (6)

Soybeans (Glycine max) (2)

3a	3kakB03	B:96-142,B:333-365
3b	3kakA03	A:96-142,A:333-365

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PreATP-grasp (8)

Family: GSH_synthase (4)

Glycine max (Soybean) (Glycine hispida) (3)

1a	GSH_synthase-3kakB01	B:229-331
1b	GSH_synthase-3kakB02	B:229-331

Clan: no clan defined [family: GSH_synth_ATP] (4)

Family: GSH_synth_ATP (4)

Glycine max (Soybean) (Glycine hispida) (3)

2a	GSH_synth_ATP-3kakB03	B:30-498
2b	GSH_synth_ATP-3kakB04	B:30-498

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9M426_SOYBN | Q9M426)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Cys A:323 - Pro A:324	[ RasMol ]
		Cys B:323 - Pro B:324	[ RasMol ]

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	3kak
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	Q9M426_SOYBN \| Q9M426
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	6.3.2.3
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	Q9M426_SOYBN \| Q9M426	:	3kaj 3kal

3kaj	HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX
3kal	HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN CLOSED CONFORMATION WITH HOMOGLUTATHIONE AND ADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (3, 6)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

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