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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOGEN SYNTHASE FROM A. TUMEFACIENS IN COMPLEX WITH ADP
 
Authors :  A. Buschiazzo, M. E. Guerin, J. E. Ugalde, R. A. Ugalde, W. Shepard, P. M.
Date :  29 Dec 03  (Deposition) - 31 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyl-Transferase, Gt-B Fold, Rossmann Fold, Adp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Buschiazzo, J. E. Ugalde, M. E. Guerin, W. Shepard, R. A. Ugalde, P. M. Alzari
Crystal Structure Of Glycogen Synthase: Homologous Enzymes Catalyze Glycogen Synthesis And Degradation.
Embo J. V. 23 3196 2004
PubMed-ID: 15272305  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600324
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOGEN SYNTHASE 1
    Chains: A, B
    EC Number: 2.4.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLGA1, GLGA, ATU4075, AGR_L_1562
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: STARCH [BACTERIAL GLYCOGEN] SYNTHASE 1

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:304 , LEU A:326 , GLY A:327 , GLY A:353 , TYR A:354 , ASN A:355 , THR A:381 , HOH A:1594BINDING SITE FOR RESIDUE ADP A 1531
2AC2SOFTWAREILE B:297 , ARG B:299 , LYS B:304 , GLY B:327 , GLY B:353 , TYR B:354 , ASN B:355 , GLU B:376 , THR B:381 , TYR B:384 , HOH B:2540 , HOH B:2564 , HOH B:2582 , HOH B:2583 , HOH B:2600BINDING SITE FOR RESIDUE ADP B 2531

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:11 -Pro A:12
2Ser A:423 -Pro A:424
3Tyr B:11 -Pro B:12
4Ser B:423 -Pro B:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RZU)

(-) 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:477
 aligned with GLGA1_RHIRD | P0A3F3 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:477
                                    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       
          GLGA1_RHIRD     1 MNVLSVSSEIYPLIKTGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAAVTDPVKCFEFTDLLGEKADLLEVQHERLDLLILDAPAYYERSGGPYLGQTGKDYPDNWKRFAALSLAAARIGAGVLPGWRPDMVHAHDWQAAMTPVYMRYAETPEIPSLLTIHNIAFQGQFGANIFSKLALPAHAFGMEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGMGLEGVIGSRAHVLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHFRIDDDGSPLFCVISRLTWQKGIDLMAEAVDEIVSLGGRLVVLGAGDVALEGALLAAASRHHGRVGVAIGYNEPLSHLMQAGCDAIIIPSRFEPCGLTQLYALRYGCIPVVARTGGLADTVIDANHAALASKAATGVQFSPVTLDGLKQAIRRTVRYYHDPKLWTQMQKLGMKSDVSWEKSAGLYAALYSQLIS 477
               SCOP domains d1rzua_ A: Glycogen synthase 1, GlgA                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1rzuA02 A:249-457 Glycogen Phosphorylase B;                                                                                                                                                                      -------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh...eeeeee.......eeeeeeee..eeeeeeehhhhhh...............hhhhhhhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhh......eeeee.......eehhhhhhhh..hhhhh.....ee..eeehhhhhhhhh.eeee.hhhhhhhh.hhhhhh.hhhhhhhhhh.eee............................hhhhhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh.eeeee.hhhhhhhh...hhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzu A   1 MNVLSVSSEIYPLIKTGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAAVTDPVKCFEFTDLLGEKADLLEVQHERLDLLILDAPAYYERSGGPYLGQTGKDYPDNWKRFAALSLAAARIGAGVLPGWRPDMVHAHDWQAAMTPVYMRYAETPEIPSLLTIHNIAFQGQFGANIFSKLALPAHAFGMEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGMGLEGVIGSRAHVLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHFRIDDDGSPLFCVISRLTWQKGIDLMAEAVDEIVSLGGRLVVLGAGDVALEGALLAAASRHHGRVGVAIGYNEPLSHLMQAGCDAIIIPSRFEPCGLTQLYALRYGCIPVVARTGGLADTVIDANHAALASKAATGVQFSPVTLDGLKQAIRRTVRYYHDPKLWTQMQKLGMKSDVSWEKSAGLYAALYSQLIS 477
                                    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       


Chain B from PDB  Type:PROTEIN  Length:478
 aligned with GLGA1_RHIRD | P0A3F3 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:478
                                    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        
          GLGA1_RHIRD     1 MNVLSVSSEIYPLIKTGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAAVTDPVKCFEFTDLLGEKADLLEVQHERLDLLILDAPAYYERSGGPYLGQTGKDYPDNWKRFAALSLAAARIGAGVLPGWRPDMVHAHDWQAAMTPVYMRYAETPEIPSLLTIHNIAFQGQFGANIFSKLALPAHAFGMEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGMGLEGVIGSRAHVLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHFRIDDDGSPLFCVISRLTWQKGIDLMAEAVDEIVSLGGRLVVLGAGDVALEGALLAAASRHHGRVGVAIGYNEPLSHLMQAGCDAIIIPSRFEPCGLTQLYALRYGCIPVVARTGGLADTVIDANHAALASKAATGVQFSPVTLDGLKQAIRRTVRYYHDPKLWTQMQKLGMKSDVSWEKSAGLYAALYSQLISK 478
               SCOP domains d1rzub_ B: Glycogen synthase 1, GlgA                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1rzuB02 B:249-457 Glycogen Phosphorylase B;                                                                                                                                                                      --------------------- CATH domains
           Pfam domains (1) -Glyco_transf_5-1rzuB01 B:2-236                                                                                                                                                                                                             --------------------------------------------Glycos_transf_1-1rzuB03 B:281-454                                                                                                                                             ------------------------ Pfam domains (1)
           Pfam domains (2) -Glyco_transf_5-1rzuB02 B:2-236                                                                                                                                                                                                             --------------------------------------------Glycos_transf_1-1rzuB04 B:281-454                                                                                                                                             ------------------------ Pfam domains (2)
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhh...eeeee.........eeeeeee..eeeeeee.....................hhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhhh......eeee........eehhhhhhhh..hhhhh.....ee..eeehhhhhhhhh.eeee.hhhhhhhh.hhhhhh.hhhhhhhhhh.eee............................hhhhhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh.eeeee.hhhhhhhh...hhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzu B   1 MNVLSVSSEIYPLIKTGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAAVTDPVKCFEFTDLLGEKADLLEVQHERLDLLILDAPAYYERSGGPYLGQTGKDYPDNWKRFAALSLAAARIGAGVLPGWRPDMVHAHDWQAAMTPVYMRYAETPEIPSLLTIHNIAFQGQFGANIFSKLALPAHAFGMEGIEYYNDVSFLKGGLQTATALSTVSPSYAEEILTAEFGMGLEGVIGSRAHVLHGIVNGIDADVWNPATDHLIHDNYSAANLKNRALNKKAVAEHFRIDDDGSPLFCVISRLTWQKGIDLMAEAVDEIVSLGGRLVVLGAGDVALEGALLAAASRHHGRVGVAIGYNEPLSHLMQAGCDAIIIPSRFEPCGLTQLYALRYGCIPVVARTGGLADTVIDANHAALASKAATGVQFSPVTLDGLKQAIRRTVRYYHDPKLWTQMQKLGMKSDVSWEKSAGLYAALYSQLISK 478
                                    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
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GT-B (132)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLGA1_RHIRD | P0A3F3)
molecular function
    GO:0033201    alpha-1,4-glucan synthase activity    Catalysis of the reaction: RDP-glucose + [alpha-D-glucosyl-(1,4)]n = RDP + [alpha-D-glucosyl-(1,4)]n+1, where RDP is ADP or UDP.
    GO:0004373    glycogen (starch) synthase activity    Catalysis of the reaction: UDP-glucose + (1,4)-alpha-D-glucosyl(n) = UDP + (1,4)-alpha-D-glucosyl(n+1).
    GO:0009011    starch synthase activity    Catalysis of the reaction: ADP-glucose + (1,4)-alpha-D-glucosyl(n) = ADP + (1,4)-alpha-D-glucosyl(n+1).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.

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  2.4.1.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLGA1_RHIRD | P0A3F3: 1rzv

(-) Related Entries Specified in the PDB File

1rzv CRYSTAL STRUCTURE OF THE GLYCOGEN SYNTHASE FROM AGROBACTERIUM TUMEFACIENS