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(-) Description

Title :  STRUCTURE OF GLYCOGEN SYNTHASE FROM PYROCOCCUS ABYSSI
 
Authors :  C. Horcajada, J. J. Guinovart, I. Fita, J. C. Ferrer
Date :  25 Jan 05  (Deposition) - 28 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Glycosyltransferase Family, 5 Udp/Adp-Glucose-Glycogen Synthase, Two Rossman Folds, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Horcajada, J. J. Guinovart, I. Fita, J. C. Ferrer
Crystal Structure Of An Archaeal Glycogen Synthase: Insights Into Oligomerisation And Substrate Binding Of Eukaryotic Glycogen Synthases.
J. Biol. Chem. V. 281 2923 2006
PubMed-ID: 16319074  |  Reference-DOI: 10.1074/JBC.M507394200

(-) 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: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: (DE3)-RIL
    Expression System Vector Type: PLASMID
    Organism Common: PYROCOCCUS ABYSSI
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1DIO10Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3GOL7Ligand/IonGLYCEROL
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3GOL3Ligand/IonGLYCEROL
4UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GLC-1Ligand/IonALPHA-D-GLUCOSE
3GOL3Ligand/IonGLYCEROL
4UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (4, 6)
No.NameCountTypeFull Name
1DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3GOL1Ligand/IonGLYCEROL
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:98 , PRO A:159 , TYR A:162BINDING SITE FOR RESIDUE GLC A 601
02AC2SOFTWAREASP C:94 , ARG C:98 , PRO C:159 , TYR C:162BINDING SITE FOR RESIDUE GLC C 602
03AC3SOFTWAREPHE A:216 , ARG A:408 , SER A:411 , LYS A:416BINDING SITE FOR RESIDUE DIO A 604
04AC4SOFTWAREILE A:199 , TRP A:202 , PHE A:433 , ILE A:436 , DIO A:606BINDING SITE FOR RESIDUE DIO A 605
05AC5SOFTWARETYR A:214 , ASP A:430 , DIO A:605BINDING SITE FOR RESIDUE DIO A 606
06AC6SOFTWARELEU A:171 , TYR A:185BINDING SITE FOR RESIDUE DIO A 607
07AC7SOFTWARESER B:411 , PHE B:412BINDING SITE FOR RESIDUE DIO B 608
08AC8SOFTWAREILE B:199 , TRP B:202 , PHE B:433 , ILE B:436 , DIO B:610BINDING SITE FOR RESIDUE DIO B 609
09AC9SOFTWARELEU B:198 , TYR B:214 , ASP B:430 , ALA B:432 , DIO B:609BINDING SITE FOR RESIDUE DIO B 610
10BC1SOFTWAREARG A:260 , GLU A:295 , LEU A:296 , PHE C:161 , HIS C:164 , GLU C:165BINDING SITE FOR RESIDUE UDP C 603
11BC2SOFTWAREPHE C:216 , ARG C:408 , SER C:411 , LYS C:416BINDING SITE FOR RESIDUE DIO C 611
12BC3SOFTWAREILE C:199 , PHE C:433 , ILE C:436BINDING SITE FOR RESIDUE DIO C 612
13BC4SOFTWARELEU C:198 , TYR C:214 , ASP C:430BINDING SITE FOR RESIDUE DIO C 613
14BC5SOFTWAREGLU A:339 , PHE A:341 , GLY A:342 , LEU A:343BINDING SITE FOR RESIDUE GOL A 614
15BC6SOFTWAREASP A:128 , TRP A:129 , HIS A:130 , ARG A:152 , ASN A:154 , GLU A:180BINDING SITE FOR RESIDUE GOL A 615
16BC7SOFTWARETRP A:224 , ARG A:319 , GLU A:347BINDING SITE FOR RESIDUE GOL A 616
17BC8SOFTWAREARG B:152 , GLU B:339 , PRO B:340 , PHE B:341BINDING SITE FOR RESIDUE GOL B 617
18BC9SOFTWARELEU B:96 , TRP B:129 , HIS B:130 , ARG B:152 , ASN B:154BINDING SITE FOR RESIDUE GOL B 618
19CC1SOFTWAREARG B:319 , VAL B:322 , TYR B:326 , GLU B:347BINDING SITE FOR RESIDUE GOL B 619
20CC2SOFTWARETYR C:89 , TRP C:129 , HIS C:130 , ASN C:154BINDING SITE FOR RESIDUE GOL C 620

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:11 -Pro A:12
2Leu B:11 -Pro B:12
3Leu C:11 -Pro C:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BIS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BIS)

(-) Exons   (0, 0)

(no "Exon" information available for 2BIS)

(-) 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:440
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:440
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
         Q9V2J8_PYRAB     - ---MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains ---d2bisa1 A:1-437 Glycogen synthase 1, GlgA                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeee....eeeeeeeeeee..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhh.hhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh...eeee....hhhhhhhhhh...eeee.......hhhhhhhhh...eeeee...hhhhhh.....eee...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bis A  -2 GSHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437


Chain B from PDB  Type:PROTEIN  Length:440
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:440
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
         Q9V2J8_PYRAB     - ---MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains d2bisb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee..eeeeeeeeeeee..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhhhhhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.......hhhhhhhhhh..eeeee..hhhhhhh.....eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bis B  -2 GSHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437


Chain C from PDB  Type:PROTEIN  Length:440
 aligned with Q9V2J8_PYRAB | Q9V2J8 from UniProtKB/TrEMBL  Length:437

    Alignment length:440
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
         Q9V2J8_PYRAB     - ---MKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
               SCOP domains d2bisc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee..eeeeeeeeeeee..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee.......eehhhhhhhhhhhhh...eehhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..eee..........hhhhh..hhhhhhhhhhhh.......eeee.........hhhhhhhhhhh....hhhhh.eeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.......hhhhhhhhhhh.eeee....hhhhhhhhhhhee....hhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bis C  -2 GSHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL 437
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BIS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BIS)

(-) Gene Ontology  (1, 1)

Asymmetric 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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  Q9V2J8_PYRAB | Q9V2J8
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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