Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  APOENZYME STRUCTURE OF HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN OPEN CONFORMATION
 
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 :  2.00
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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3KAJ)

(-) Sites  (0, 0)

(no "Site" information available for 3KAJ)

(-) SS Bonds  (0, 0)

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

(-) 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 3KAJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KAJ)

(-) 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:452
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:471
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498 
         Q9M426_SOYBN    29 FDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------3kajA02     3kajA03 A:96-142,A:333-    365                 3kajA02 A:84-95,A:143-182,A:443-498     --------------------------3kajA04 A:209-332  [code=3.40.50.1760, no name defined]                                                                     3kajA03 A:96-142,A:333-365       -------------------------      ---------------         ----------------------3kajA02 A:84-95,A:143-182,A:443-498                     - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..eee..............eee..ee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----..hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh....eeeehhhhhhhheee.....eee..eeeeeeee....hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhh..eee............hhh.eeee..------..hhhhhhhhhh...---------.eeee......eeeeeee..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.............eee.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kaj A  29 FDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESL----NADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQ------NIYGDELRETLLKLQ---------YILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
                                    38        48        58        68        78        88        98       108       118    |  128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388 |     398       408  |      -  |    428       438       448       458       468       478       488       498 
                                                                                                                   118  123                                                                                                                                                                                                                                                                        390    397           411       421                                                                              


Chain B from PDB  Type:PROTEIN  Length:442
 aligned with Q9M426_SOYBN | Q9M426 from UniProtKB/TrEMBL  Length:499

    Alignment length:471
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498 
         Q9M426_SOYBN    29 FDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESLSRTKNADEFTSRLLDIHSKMLQINKKEDIRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQREGGGNNIYGDELRETLLKLQEAGSQEDAAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISSSYEGGVLPGFGVVDTVYLT 499
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------3kajB02     3kajB03 B:96-142,B:333-      365               3   kajB02 B:84-95,B:143-182,B:443-498  --------------------------3kajB04 B:209-332  [code=3.40.50.1760, no name defined]                                                                     3kajB03 B:96-142,B:333-365       --------------------------   -----------------       ------------------------3kajB02 B:84-95,B:143-182,B:443-498                     - CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kajB01 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSH_synthase-3kajB02 B:229-331                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) GSH_synth_ATP-3kajB03 B:29-498                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (3)
           Pfam domains (4) GSH_synth_ATP-3kajB04 B:29-498                                                                                                                                                                                                                                                                                                                                                                                                                                                        - Pfam domains (4)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..eee..............eee..ee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------hhhhhhhhhhhhhhhhhh.---.eeeeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh....eeeehhhhhhhhhee.....eee..eeeeeeee....hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..ee.......hhhhhhhhh.eee....---.........hhhhhh..-------....eee......eeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee..----------.eee.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kaj B  29 FDYHRIDQKLLQNIVYDALVWSTLNCLLVGDKSVQRSGRVPGVGLVHLPLSLLPGPFPESHWKQGCELAPIFNELVDRVSLDGKFLQESL------DEFTSRLLDIHSKMLQINK---IRMGIVRSDYMIDEKTKSLLQIEMNTISTSFALIGCLMTGLHKSLLSQYGKFLGLNSNRVPANNAVDQSAEALAKAWSEYNNPRAAILVVVQVEERNMYEQHYISALLREKHHIRSIRKTLTEIDQEGKILPDGTLSVDGQAISVVYFRAGYTPKDYPSESEWRARLLMEQSSAIKCPTISYHLVGTKKIQQELAKPGVLERFVENKDHIAKLRACFAGLWSLEDSDIVKKAIENPELFVMKPQR---GNNIYGDELRETLLKLQ-------AAYILMQRIFPATSPAILVRDGNWDTGHVISEAGIFGTYLRNKDKIIINNESGYMVRTKISS----------GVVDTVYLT 499
                                    38        48        58        68        78        88        98       108       118      |128       138    |  148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388  |   |398       408  |      -|      428       438       448       458       468       478 |       -  |    498 
                                                                                                                   118    125               143 147                                                                                                                                                                                                                                                 391 395             411     419                                                          480        491
   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 3KAJ)

(-) CATH Domains  (3, 6)

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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3kaj)
 
  Sites
(no "Sites" information available for 3kaj)
 
  Cis Peptide Bonds
    Cys A:323 - Pro A:324   [ RasMol ]  
    Cys B:323 - Pro B:324   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3kaj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9M426_SOYBN | Q9M426
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9M426_SOYBN | Q9M426
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9M426_SOYBN | Q9M426: 3kak 3kal

(-) Related Entries Specified in the PDB File

3kak HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN OPEN CONFORMATION WITH GAMMA-GLUTAMYL-CYSTEINE BOUND
3kal HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN CLOSED CONFORMATION WITH HOMOGLUTATHIONE AND ADP