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(-) Description

Title :  STRUCTURE OF HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN CLOSED CONFORMATION WITH HOMOGLUTATHIONE, ADP, A SULFATE ION, AND THREE MAGNESIUM IONS 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 :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Atp-Grasp Domain, Homoglutathione (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)

(-) Compounds

Molecule 1 - HOMOGLUTATHIONE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2HGS4Ligand/IonD-GAMMA-GLUTAMYL-L-CYSTEINYL-BETA-ALANINE
3MG6Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:168 , GLU A:169 , LYS A:334 , VAL A:386 , LYS A:388 , GLU A:392 , GLY A:393 , GLY A:394 , ASN A:397 , TYR A:399 , MET A:424 , GLN A:425 , ARG A:426 , ILE A:427 , GLU A:450 , LYS A:477 , MG A:502 , MG A:503 , SO4 A:505 , HOH A:588 , HOH A:650 , HOH A:683 , HOH A:710 , HOH A:734 , HOH A:864BINDING SITE FOR RESIDUE ADP A 500
02AC2SOFTWAREARG A:153 , ASN A:171 , ILE A:173 , SER A:174 , THR A:175 , SER A:176 , PHE A:177 , GLN A:238 , GLU A:241 , ASN A:243 , ARG A:295 , TYR A:298 , ARG A:475 , VAL A:486 , LEU A:487 , SO4 A:505 , HOH A:688 , HOH A:835BINDING SITE FOR RESIDUE HGS A 501
03AC3SOFTWAREGLU A:169 , ASN A:171 , GLU A:392 , ADP A:500 , SO4 A:505BINDING SITE FOR RESIDUE MG A 502
04AC4SOFTWAREGLU A:169 , ADP A:500 , SO4 A:505 , HOH A:588 , HOH A:710BINDING SITE FOR RESIDUE MG A 503
05AC5SOFTWAREGLU A:169 , MET A:170 , GLY A:332 , GLU A:392 , HOH A:566 , HOH A:634BINDING SITE FOR RESIDUE MG A 504
06AC6SOFTWAREARG A:153 , ASP A:155 , GLU A:169 , ASN A:171 , GLU A:392 , GLY A:393 , ARG A:475 , ADP A:500 , HGS A:501 , MG A:502 , MG A:503 , HOH A:588 , HOH A:710BINDING SITE FOR RESIDUE SO4 A 505
07AC7SOFTWARETRP A:49 , ASN A:53 , CYS A:182 , LEU A:183 , GLY A:186 , ASN A:209 , ASN A:210 , VAL A:212 , ASP A:213 , HOH A:658 , HOH A:675 , HOH A:747 , HOH A:828 , HOH A:854 , HOH A:861BINDING SITE FOR RESIDUE HGS A 506
08AC8SOFTWAREILE B:168 , GLU B:169 , LYS B:334 , VAL B:386 , LYS B:388 , ARG B:391 , GLU B:392 , GLY B:393 , GLY B:394 , ASN B:396 , ASN B:397 , TYR B:399 , MET B:424 , GLN B:425 , ARG B:426 , ILE B:427 , GLU B:450 , LYS B:477 , MG B:502 , MG B:503 , SO4 B:505 , HOH B:627 , HOH B:663 , HOH B:684 , HOH B:758 , HOH B:800BINDING SITE FOR RESIDUE ADP B 500
09AC9SOFTWAREARG B:153 , ASN B:171 , ILE B:173 , SER B:174 , THR B:175 , SER B:176 , GLN B:238 , GLU B:241 , ASN B:243 , ARG B:295 , TYR B:298 , ARG B:475 , GLY B:485 , VAL B:486 , SO4 B:505 , HOH B:545 , HOH B:551 , HOH B:688 , HOH B:807BINDING SITE FOR RESIDUE HGS B 501
10BC1SOFTWAREGLU B:169 , ASN B:171 , GLU B:392 , ADP B:500 , SO4 B:505BINDING SITE FOR RESIDUE MG B 502
11BC2SOFTWAREGLU B:169 , ADP B:500 , SO4 B:505 , HOH B:627 , HOH B:663BINDING SITE FOR RESIDUE MG B 503
12BC3SOFTWAREGLU B:169 , MET B:170 , GLY B:332 , GLU B:392 , HOH B:537BINDING SITE FOR RESIDUE MG B 504
13BC4SOFTWAREARG B:153 , ASP B:155 , GLU B:169 , ASN B:171 , GLU B:392 , GLY B:393 , ARG B:475 , ADP B:500 , HGS B:501 , MG B:502 , MG B:503 , HOH B:627 , HOH B:663BINDING SITE FOR RESIDUE SO4 B 505
14BC5SOFTWAREASN B:53 , CYS B:182 , LEU B:183 , ASP B:213 , HOH B:536 , HOH B:655 , HOH B:828 , HOH B:834BINDING SITE FOR RESIDUE HGS B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:323 -Pro A:324
2Cys B:323 -Pro B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KAL)

(-) Sequences/Alignments

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:470
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:475
                                    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       494     
         Q9M426_SOYBN    25 APPLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------3kalA02     3kalA03 A:96-142,A:333-365                     3kalA02 A:84-95,A:143-182,A:443-498     --------------------------3kalA04 A:209-332  [code=3.40.50.1760, no name defined]                                                                     3kalA03 A:96-142,A:333-365       3kalA05 A:366-431  [code=3.30.1490.50, no name      defined]      -----------3kalA02 A:84-95,A:143-182,A:443-498                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh..eee..............eee..ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhheee.....eee..eeeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhh..eee....hhhhhhhhh...eeee..........hhhhhhhhhhhh.-----hhhh.eeee......eeeeeee..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.............eee.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kal A  25 APPLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQ-----EDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
                                    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      |  -  |    424       434       444       454       464       474       484       494     
                                                                                                                                                                                                                                                                                                                                                                                                                            411   417                                                                                  


Chain B from PDB  Type:PROTEIN  Length:468
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:475
                                    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       494     
         Q9M426_SOYBN    25 APPLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------3kalB02     3kalB03 B:96-142,B:333-365                     3kalB02 B:84-95,B:143-182,B:443-498     --------------------------3kalB04 B:209-332  [code=3.40.50.1760, no name defined]                                                                     3kalB03 B:96-142,B:333-365       3kalB05 B:366-431  [code=3.30.1490.50, no na       me defined]    -----------3kalB02 B:84-95,B:143-182,B:443-498                     - CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kalB01 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kalB02 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----GSH_synth_ATP-3kalB03 B:29-498                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (3)
           Pfam domains (4) ----GSH_synth_ATP-3kalB04 B:29-498                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (4)
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh..eee..............eee..ee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhh....eeeehhhhhhhheee.....eee..eeeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..eee..hhhhhhhhhhh...eeee..........hhhhhhhhhhh-------.....eeee......eeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee.............eee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kal B  25 APPLFDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLK-------EDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
                                    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    |    -  |    424       434       444       454       464       474       484       494     
                                                                                                                                                                                                                                                                                                                                                                                                                          409     417
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3KAL)

(-) CATH Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: PreATP-grasp (8)
(-)
Clan: no clan defined [family: GSH_synth_ATP] (4)

(-) Gene Ontology  (9, 9)

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.

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  3kal
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9M426_SOYBN | Q9M426: 3kaj 3kak

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KAL)