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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOGEN SYNTHASE FROM AGROBACTERIUM TUMEFACIENS (NON-COMPLEXED FORM)
 
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) - 12 Nov 14  (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, 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: AGROBACTERIUM TUMEFACIENS
    Expression System Plasmid: PBBRMCS-4
    Expression System Strain: A5130
    Expression System Taxid: 358
    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, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1RZV)

(-) SS Bonds  (0, 0)

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

(-) 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 1RZV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RZV)

(-) 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 d1rzva_ A: Glycogen synthase 1, GlgA                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1rzvA02 A:249-457 Glycogen Phosphorylase B;                                                                                                                                                                      -------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhhh...eeeeeee.hhhhhh.....eeeeee.......eeeeeee....eeeeeehhhhhh...............hhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhh......eeeee.......eehhhhhhhh..hhhhhh....ee..eeehhhhhhhhh.eeee.hhhhhhhh.hhhhhh.hhhhhhhhhh.eee......................hhhhhhhhhhhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh.eeeee.hhhhhhhh...hhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzv 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       
                            |                                                                                                                                 133-MSE   143-MSE|                                     188-MSE                                 228-MSE                                                                          309-MSE                                              362-MSE                                                                                 450-MSE|                      
                            1-MSE                                                                                                                                            148-MSE                                                                                                                                                                                                                                                                                                            455-MSE                  


Chain B 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 d1rzvb_ B: Glycogen synthase 1, GlgA                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1rzvB02 B:249-457 Glycogen Phosphorylase B;                                                                                                                                                                      -------------------- CATH domains
           Pfam domains (1) -Glyco_transf_5-1rzvB01 B:2-236                                                                                                                                                                                                             --------------------------------------------Glycos_transf_1-1rzvB03 B:281-454                                                                                                                                             ----------------------- Pfam domains (1)
           Pfam domains (2) -Glyco_transf_5-1rzvB02 B:2-236                                                                                                                                                                                                             --------------------------------------------Glycos_transf_1-1rzvB04 B:281-454                                                                                                                                             ----------------------- Pfam domains (2)
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh....eeeee.......eeeeeeee..eeeeeeehhhhhh...............hhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhh......eeeee.......eehhhhhhhh..hhhhh.....ee..eeehhhhhhhhh.eeee.hhhhhhhh.hhhhhh.hhhhhhhhhh.eee......................hhhhhhhhhhhhhhhhhhh........eeeee.......hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh.eeeee.hhhhhhh....hhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzv B   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       
                            1-MSE                                                                                                                             133-MSE   143-MSE|                                     188-MSE                                 228-MSE                                                                          309-MSE                                              362-MSE                                                                                 450-MSE|                      
                                                                                                                                                                             148-MSE                                                                                                                                                                                                                                                                                                            455-MSE
   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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 Related Entries

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

UniProtKB/Swiss-Prot
        GLGA1_RHIRD | P0A3F3: 1rzu

(-) Related Entries Specified in the PDB File

1rzu CRYSTAL STRUCTURE OF THE GLYCOGEN SYNTHASE FROM A. TUMEFACIENS IN COMPLEX WITH ADP