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(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-GLUTAMYLCYSTEINE SYNTHETASE FROM ESCHERICHIA COLI B COMPLEXED WITH TRANSITION-STATE ANALOGUE
 
Authors :  T. Hibi, H. Nii, T. Nakatsu, H. Kato, J. Hiratake, J. Oda
Date :  12 Feb 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glutathione Homeostasis, Beta Barrel, Peptide Synthesis, Transition State Analogue, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hibi, H. Nii, T. Nakatsu, A. Kimura, H. Kato, J. Hiratake, J. Oda
Crystal Structure Of Gamma-Glutamylcysteine Synthetase: Insights Into The Mechanism Of Catalysis By A Key Enzyme For Glutathione Homeostasis
Proc. Natl. Acad. Sci. Usa V. 101 15052 2004
PubMed-ID: 15477603  |  Reference-DOI: 10.1073/PNAS.0403277101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE--CYSTEINE LIGASE
    ChainsA, B
    EC Number6.3.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKGC20
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGSH-I
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymGAMMA-GLUTAMYLCYSTEINE SYNTHETASE, GAMMA-ECS, GCS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG8Ligand/IonMAGNESIUM ION
3P2S2Ligand/Ion(2S)-2-AMINO-4-[[(2R)-2-CARBOXYBUTYL](PHOSPHONO)SULFONIMIDOYL]BUTANOIC ACID
4P6G2Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3P2S1Ligand/Ion(2S)-2-AMINO-4-[[(2R)-2-CARBOXYBUTYL](PHOSPHONO)SULFONIMIDOYL]BUTANOIC ACID
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3P2S1Ligand/Ion(2S)-2-AMINO-4-[[(2R)-2-CARBOXYBUTYL](PHOSPHONO)SULFONIMIDOYL]BUTANOIC ACID
4P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:29 , ASP A:60 , GLU A:67 , P2S A:520 , MG A:524 , HOH A:571BINDING SITE FOR RESIDUE MG A 522
02AC2SOFTWAREGLU A:27 , HIS A:150 , GLU A:328 , P2S A:520 , ADP A:521 , MG A:524BINDING SITE FOR RESIDUE MG A 523
03AC3SOFTWAREGLU A:27 , GLU A:67 , P2S A:520 , ADP A:521 , MG A:522 , MG A:523 , HOH A:705BINDING SITE FOR RESIDUE MG A 524
04AC4SOFTWAREASP A:408 , HOH A:546 , HOH A:574 , HOH A:696 , HOH B:1628 , HOH B:1643BINDING SITE FOR RESIDUE MG A 525
05AC5SOFTWAREGLU B:29 , ASP B:60 , GLU B:67 , P2S B:1520 , MG B:1524 , HOH B:1657BINDING SITE FOR RESIDUE MG B 1522
06AC6SOFTWAREGLU B:27 , HIS B:150 , GLU B:328 , P2S B:1520 , ADP B:1521BINDING SITE FOR RESIDUE MG B 1523
07AC7SOFTWAREGLU B:27 , GLU B:67 , P2S B:1520 , ADP B:1521 , MG B:1522 , HOH B:1677BINDING SITE FOR RESIDUE MG B 1524
08AC8SOFTWAREHOH A:709 , ASP B:408 , HOH B:1664 , HOH B:1666 , HOH B:1667 , HOH B:1678BINDING SITE FOR RESIDUE MG B 1525
09AC9SOFTWAREGLU A:27 , GLU A:29 , ASP A:60 , GLU A:67 , TYR A:131 , LEU A:135 , GLN A:144 , ILE A:146 , SER A:147 , GLY A:148 , HIS A:150 , ARG A:235 , TYR A:241 , TYR A:300 , GLU A:328 , ARG A:330 , ADP A:521 , MG A:522 , MG A:523 , MG A:524 , P6G A:526 , HOH A:570 , HOH A:584 , HOH A:697 , HOH A:705BINDING SITE FOR RESIDUE P2S A 520
10BC1SOFTWAREGLN A:23 , GLY A:25 , LEU A:26 , GLU A:27 , GLU A:67 , ILE A:69 , THR A:70 , PRO A:71 , VAL A:72 , ASN A:152 , SER A:154 , LYS A:306 , GLU A:325 , TYR A:326 , GLU A:328 , P2S A:520 , MG A:523 , MG A:524 , HOH A:538 , HOH A:549 , HOH A:564 , HOH A:584 , HOH A:614 , HOH A:683 , HOH A:693 , HOH A:705BINDING SITE FOR RESIDUE ADP A 521
11BC2SOFTWARETYR A:188 , ARG A:235 , LEU A:236 , TYR A:300 , ARG A:330 , LEU A:370 , ARG A:374 , TRP A:377 , P2S A:520 , HOH A:644 , HOH A:645BINDING SITE FOR RESIDUE P6G A 526
12BC3SOFTWAREGLU B:27 , GLU B:29 , ASP B:60 , GLU B:67 , TYR B:131 , LEU B:135 , GLN B:144 , ILE B:146 , SER B:147 , GLY B:148 , HIS B:150 , ARG B:235 , TYR B:241 , ASN B:297 , TYR B:300 , GLU B:328 , ARG B:330 , ADP B:1521 , MG B:1522 , MG B:1523 , MG B:1524 , P6G B:1526 , HOH B:1555 , HOH B:1658 , HOH B:1677BINDING SITE FOR RESIDUE P2S B 1520
13BC4SOFTWAREGLN B:23 , GLY B:25 , LEU B:26 , GLU B:27 , GLU B:67 , ILE B:69 , THR B:70 , PRO B:71 , VAL B:72 , ASN B:152 , PHE B:153 , SER B:154 , LYS B:306 , GLU B:325 , TYR B:326 , GLU B:328 , P2S B:1520 , MG B:1523 , MG B:1524 , HOH B:1613 , HOH B:1655 , HOH B:1658 , HOH B:1661 , HOH B:1677BINDING SITE FOR RESIDUE ADP B 1521
14BC5SOFTWARETYR B:188 , ARG B:235 , LEU B:236 , TYR B:300 , ARG B:330 , ARG B:374 , TRP B:377 , P2S B:1520 , HOH B:1632 , HOH B:1633BINDING SITE FOR RESIDUE P6G B 1526

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:372 -A:395
2B:372 -B:395

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VA6)

(-) Exons   (0, 0)

(no "Exon" information available for 1VA6)

(-) Sequences/Alignments

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:507
 aligned with GSH1_ECOLI | P0A6W9 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:515
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     
           GSH1_ECOLI     1 MIPDVSQALAWLEKHPQALKGIQRGLERETLRVNADGTLATTGHPEALGSALTHKWITTDFAEALLEFITPVDGDIEHMLTFMRDLHRYTARNMGDERMWPLSMPCYIAEGQDIELAQYGTSNTGRFKTLYREGLKNRYGALMQTISGVHYNFSLPMAFWQAKCGDISGADAKEKISAGYFRVIRNYYRFGWVIPYLFGASPAICSSFLQGKPTSLPFEKTECGMYYLPYATSLRLSDLGYTNKSQSNLGITFNDLYEYVAGLKQAIKTPSEEYAKIGIEKDGKRLQINSNVLQIENELYAPIRPKRVTRSGESPSDALLRGGIEYIEVRSLDINPFSPIGVDEQQVRFLDLFMVWCALADAPEMSSSELACTRVNWNRVILEGRKPGLTLGIGCETAQFPLPQVGKDLFRDLKRVAQTLDSINGGEAYQKVCDELVACFDNPDLTFSARILRSMIDTGIGGTGKAFAEAYRNLLREEPLEILREEDFVAEREASERRQQEMEAADTEPFAVWLE 515
               SCOP domains d1va6a_ A: Gamma-glutamylcysteine synthetase GshA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh..eeeeeeeeeee...........hhhhh.......eee.....eeeee.....hhhhhhhhhhhhhhhhhh.....ee......................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhh----.....ee.....ee.....hhhhh.....hhhhh.......hhhhhhhhhhhhhh..hhhhhh...ee..ee.........hhhhh...eeee.......hhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....ee........eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1va6 A   1 MIPDVSQALAWLEKHPQALKGIQRGLERETLRVNADGTLATTGHPEALGSALTHKWITTDFAEALLEFITPVDGDIEHMLTFMRDLHRYTARNMGDERMWPLSMPSYIAEGQDIELAQYGTSNTGRFKTLYREGLKNRYGALMQTISGVHYNFSLPMAFWQAKSGDISGADAKEKISAGYFRVIRNYYRFGWVIPYLFGASPAISSSFL----TSLPFEKTESGMYYLPYATSLRLSDLGYTNKSQSNLGITFNDLYEYVAGLKQAIKTPSEEYAKIGIEKDGKRLQINSNVLQIENELYAPIRPKRVTRSGESPSDALLRGGIEYIEVRSLDINPFSPIGVDEQQVRFLDLFMVWCALADAPEMSSSELACTRVNWNRVILEGRKPGLTLGIGCETAQFPLPQVGKDLFRDLKRVAQTLDSINGGEAYQKVCDELVACFDNPDLTFSARILRSMIDT----TGKAFAEAYRNLLREEPLEILREEDFVAEREASERRQQEMEAADTEPFAVWLE 515
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        |-   |   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       | -  |    470       480       490       500       510     
                                                                                                                                                                                                                                          209  214                                                                                                                                                                                                                                                 458  463                                                    

Chain B from PDB  Type:PROTEIN  Length:503
 aligned with GSH1_ECOLI | P0A6W9 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:515
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     
           GSH1_ECOLI     1 MIPDVSQALAWLEKHPQALKGIQRGLERETLRVNADGTLATTGHPEALGSALTHKWITTDFAEALLEFITPVDGDIEHMLTFMRDLHRYTARNMGDERMWPLSMPCYIAEGQDIELAQYGTSNTGRFKTLYREGLKNRYGALMQTISGVHYNFSLPMAFWQAKCGDISGADAKEKISAGYFRVIRNYYRFGWVIPYLFGASPAICSSFLQGKPTSLPFEKTECGMYYLPYATSLRLSDLGYTNKSQSNLGITFNDLYEYVAGLKQAIKTPSEEYAKIGIEKDGKRLQINSNVLQIENELYAPIRPKRVTRSGESPSDALLRGGIEYIEVRSLDINPFSPIGVDEQQVRFLDLFMVWCALADAPEMSSSELACTRVNWNRVILEGRKPGLTLGIGCETAQFPLPQVGKDLFRDLKRVAQTLDSINGGEAYQKVCDELVACFDNPDLTFSARILRSMIDTGIGGTGKAFAEAYRNLLREEPLEILREEDFVAEREASERRQQEMEAADTEPFAVWLE 515
               SCOP domains d1va6b_ B: Gamma-glutamylcysteine synthetase GshA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh..eeeeeeeeeee...........hhhhh.......eee.....eeeee.....hhhhhhhhhhhhhhhhhhh....ee......................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhh----.....ee.....ee.....hhhhh.....hhhhh.......hhhhhhhhhhhhh...hhhhhh...ee..ee.........hhhhh...eeee.......hhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....ee........eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1va6 B   1 MIPDVSQALAWLEKHPQALKGIQRGLERETLRVNADGTLATTGHPEALGSALTHKWITTDFAEALLEFITPVDGDIEHMLTFMRDLHRYTARNMGDERMWPLSMPSYIAEGQDIELAQYGTSNTGRFKTLYREGLKNRYGALMQTISGVHYNFSLPMAFWQAKSG----ADAKEKISAGYFRVIRNYYRFGWVIPYLFGASPAISSSFL----TSLPFEKTESGMYYLPYATSLRLSDLGYTNKSQSNLGITFNDLYEYVAGLKQAIKTPSEEYAKIGIEKDGKRLQINSNVLQIENELYAPIRPKRVTRSGESPSDALLRGGIEYIEVRSLDINPFSPIGVDEQQVRFLDLFMVWCALADAPEMSSSELACTRVNWNRVILEGRKPGLTLGIGCETAQFPLPQVGKDLFRDLKRVAQTLDSINGGEAYQKVCDELVACFDNPDLTFSARILRSMIDT----TGKAFAEAYRNLLREEPLEILREEDFVAEREASERRQQEMEAADTEPFAVWLE 515
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |  170       180       190       200        |-   |   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       | -  |    470       480       490       500       510     
                                                                                                                                                                                              165  170                                    209  214                                                                                                                                                                                                                                                 458  463                                                    

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VA6)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GSH1_ECOLI | P0A6W9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004357    glutamate-cysteine ligase activity    Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 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: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.
biological process
    GO:0071243    cellular response to arsenic-containing substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0071288    cellular response to mercury ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
    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.
    GO:0006972    hyperosmotic response    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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

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        GSH1_ECOLI | P0A6W91v4g 2d32 2d33

(-) Related Entries Specified in the PDB File

1v4g UNLIGANDED STRUCTURE