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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI GLYCOGEN SYNTHASE WITH OPEN AND CLOSED CONFORMATIONS
 
Authors :  A. Diaz, J. J. Guinovart, I. Fita, J. C. Ferrer
Date :  08 Jan 09  (Deposition) - 12 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Glycosyltransferase Family, Udp/Adp-Glucose-Glycogen Synthase, Two Rossman Folds, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Diaz, J. J. Guivovart, I. Fita, J. C. Ferrer
Crystal Structure Of Pyrococcus Abyssi Glycogen Synthase With Open And Closed Conformations
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLGA GLYCOGEN SYNTHASE
    Chains: A, B, C
    EC Number: 2.4.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD I
    Expression System Strain: BL21 (DE3)/PG-TF2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1NHF1Ligand/Ion1,5-ANHYDRO-D-FRUCTOSE
2PO43Ligand/IonPHOSPHATE ION
3TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:17 , HIS B:151 , ASN B:217 , LYS B:263 , GLU B:339 , GLY B:342 , LEU B:343BINDING SITE FOR RESIDUE NHF B 438
2AC2SOFTWAREPRO A:12 , ARG A:45 , LYS C:243 , PHE C:244 , PHE C:321BINDING SITE FOR RESIDUE TRS A 7360
3AC3SOFTWARETYR A:89 , LEU A:96 , TRP A:129 , HIS A:130 , ARG A:152 , ASN A:154 , GLN B:62BINDING SITE FOR RESIDUE TRS A 7361
4AC4SOFTWAREASP A:293 , ARG B:55 , GLY B:58 , ARG B:105BINDING SITE FOR RESIDUE TRS B 7362
5AC5SOFTWAREILE A:199 , TRP A:202 , PHE A:433BINDING SITE FOR RESIDUE PO4 A 8000
6AC6SOFTWAREILE B:199 , TRP B:202 , ILE B:436BINDING SITE FOR RESIDUE PO4 B 8001
7AC7SOFTWARETRP C:202 , ASP C:434BINDING SITE FOR RESIDUE PO4 C 8002

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:221 -A:350
2B:221 -B:350
3C:221 -C:350

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:11 -Pro A:12
2Gly A:90 -Pro A:91
3Leu B:11 -Pro B:12
4Gly B:90 -Pro B:91
5Leu C:11 -Pro C:12
6Gly C:90 -Pro C:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FRO)

(-) 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:439
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:439
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        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         
         Q9V2J8_PYRAB     - --MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains d3froa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee..eeeeeeeeeeee..eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhh.hhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.......hhhhhhhhhh..eeeee..hhhhhhh.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fro A  -1 RHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     8        18        28        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         


Chain B from PDB  Type:PROTEIN  Length:439
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:439
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        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         
         Q9V2J8_PYRAB     - --MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains d3frob_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee..eeeeeeeeeeee..eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhh.hhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eeee.......hhhhhhhhhhh.eeeee..hhhhhhhhhhhheee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fro B  -1 RHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     8        18        28        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         


Chain C from PDB  Type:PROTEIN  Length:439
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:439
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        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         
         Q9V2J8_PYRAB     - --MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains d3froc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee..eeeeeeeeeeee..eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhh.hhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.......hhhhhhhhhh..eeeee..hhhhhhh.....eee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fro C  -1 RHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     8        18        28        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
   Legend:   → Mismatch (orange background)
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    → 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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FRO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FRO)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q9V2J8_PYRAB | Q9V2J8)
molecular function
    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).

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  3fro
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  Q9V2J8_PYRAB | Q9V2J8
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  2.4.1.21
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 Related Entries

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

UniProtKB/TrEMBL
        Q9V2J8_PYRAB | Q9V2J8: 2bfw 2bis 3l01 4s0v 4zj8 4zjc 5u09

(-) Related Entries Specified in the PDB File

1rzu THE SAME ENZYME FROM AGROBACTERIUM TUMEFACIENS IN COMPLEX WITH ADP
2bis THE SAME PROTEIN AT LOWER RESOLUTION
2qzs THE SAME ENZYME FRON ESCHERICHIA COLI IN COMPLEX WITH ADP AND GLUCOSE