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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI GS MUTANT E377A IN COMPLEX WITH ADP AND OLIGOSACCHARIDES
 
Authors :  F. Sheng, J. H. Geiger
Date :  23 Apr 08  (Deposition) - 28 Apr 09  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyl-Transferase, Gt-B Fold, Rossmann Fold, Closed-Form, Adp And Oligosaccharide Binding, Glycogen Biosynthesis, Glycosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Sheng, A. Yep, L. Feng, J. Preiss, J. H. Geiger
Oligosaccharide Binding In Escherichia Coli Glycogen Synthase.
Biochemistry V. 48 10089 2009
PubMed-ID: 19761218  |  Reference-DOI: 10.1021/BI900916T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOGEN SYNTHASE
    Chains: A
    EC Number: 2.4.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLGA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: STARCH [BACTERIAL GLYCOGEN] SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 32)

Asymmetric/Biological Unit (6, 32)
No.NameCountTypeFull Name
12501Ligand/Ion(2R)-2-HYDROXY-3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3BGC1Ligand/IonBETA-D-GLUCOSE
4ETE12Ligand/Ion2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
5GLC15Ligand/IonALPHA-D-GLUCOSE
6NA2Ligand/IonSODIUM ION

(-) Sites  (61, 61)

Asymmetric Unit (61, 61)
No.NameEvidenceResiduesDescription
01AC1unknownGLU A:9 , THR A:16 , GLY A:17 , GLY A:18 , LEU A:19 , ASP A:137 , HIS A:139 , HIS A:161 , ASN A:162BINDING SITE FOR RESIDUE GLC A 501
02AC2unknownTHR A:16 , TYR A:95 , TRP A:138 , HIS A:139 , ARG A:300BINDING SITE FOR RESIDUE GLC A 502
03AC3unknownHIS A:96 , LEU A:100 , TYR A:165 , ARG A:300 , THR A:302BINDING SITE FOR RESIDUE GLC A 503
04AC4unknownMET A:168 , PHE A:169 , TYR A:170 , GLN A:194BINDING SITE FOR RESIDUE GLC A 504
05AC5unknownTYR A:103 , THR A:104 , PHE A:169 , TYR A:170 , HIS A:173BINDING SITE FOR RESIDUE GLC A 505
06AC7unknownGLN A:55 , PHE A:127 , HOH A:572BINDING SITE FOR RESIDUE GLC A 507
07AC8unknownARG A:38 , GLN A:55 , PHE A:71 , ASP A:125 , PHE A:127BINDING SITE FOR RESIDUE GLC A 508
08AC9unknownARG A:38 , PHE A:127BINDING SITE FOR RESIDUE GLC A 509
09AD1SOFTWAREGLU A:9 , THR A:16 , GLY A:17 , GLY A:18 , LEU A:19 , ASP A:137 , HIS A:139 , HIS A:161 , ASN A:162 , ADP A:500 , GLC A:502BINDING SITE FOR RESIDUE GLC A 501
10AD2SOFTWARETHR A:16 , TYR A:95 , TRP A:138 , HIS A:139 , ARG A:300 , GLC A:501 , GLC A:503BINDING SITE FOR RESIDUE GLC A 502
11AD3SOFTWAREHIS A:96 , LEU A:100 , TYR A:165 , ARG A:300 , THR A:302 , GLC A:502 , ETE A:527BINDING SITE FOR RESIDUE GLC A 503
12AD4SOFTWAREMET A:168 , PHE A:169 , TYR A:170 , GLN A:194 , GLC A:505BINDING SITE FOR RESIDUE GLC A 504
13AD5SOFTWARETYR A:103 , THR A:104 , PHE A:169 , TYR A:170 , HIS A:173 , GLC A:504BINDING SITE FOR RESIDUE GLC A 505
14AD6SOFTWAREGLC A:507 , ETE A:524BINDING SITE FOR RESIDUE GLC A 506
15AD7SOFTWAREGLN A:55 , VAL A:56 , PHE A:127 , GLC A:506 , GLC A:508 , ETE A:524 , HOH A:572BINDING SITE FOR RESIDUE GLC A 507
16AD8SOFTWAREARG A:38 , GLN A:55 , PHE A:71 , ASP A:125 , PHE A:127 , GLC A:507 , GLC A:509BINDING SITE FOR RESIDUE GLC A 508
17AD9SOFTWAREARG A:38 , PHE A:127 , GLC A:508 , GLC A:510BINDING SITE FOR RESIDUE GLC A 509
18AE1SOFTWAREGLC A:509 , ETE A:524BINDING SITE FOR RESIDUE GLC A 510
19AE2SOFTWAREILE A:186 , LYS A:199 , GLY A:230 , GLN A:234 , GLC A:512 , BGC A:516 , HOH A:580 , HOH A:655BINDING SITE FOR RESIDUE GLC A 511
20AE3SOFTWAREGLU A:190 , PHE A:191 , LYS A:199 , GLY A:227 , MET A:228 , GLU A:229 , GLY A:230 , LEU A:231 , GLC A:511 , GLC A:513 , HOH A:676BINDING SITE FOR RESIDUE GLC A 512
21AE4SOFTWAREILE A:186 , GLU A:190 , PHE A:191 , ASN A:192 , GLC A:512 , GLC A:514 , HOH A:676BINDING SITE FOR RESIDUE GLC A 513
22AE5SOFTWAREILE A:186 , GLC A:513 , GLC A:515BINDING SITE FOR RESIDUE GLC A 514
23AE6SOFTWAREHIS A:187 , GLC A:514 , BGC A:516BINDING SITE FOR RESIDUE GLC A 515
24AE7SOFTWAREHIS A:187 , GLC A:511 , GLC A:515BINDING SITE FOR RESIDUE BGC A 516
25AE8SOFTWAREARG A:300 , ADP A:500 , HOH A:629BINDING SITE FOR RESIDUE NA A 518
26AE9SOFTWARETHR A:209 , ALA A:210 , VAL A:244 , TYR A:469BINDING SITE FOR RESIDUE NA A 519
27AF1SOFTWARELYS A:15 , GLY A:17 , GLY A:18 , ASP A:21 , SER A:299 , ARG A:300 , LYS A:305 , LEU A:327 , GLY A:328 , GLY A:354 , TYR A:355 , HIS A:356 , LEU A:381 , THR A:382 , TYR A:385 , GLC A:501 , NA A:518 , ETE A:521 , HOH A:533 , HOH A:609 , HOH A:629 , HOH A:634BINDING SITE FOR RESIDUE ADP A 500
28AF2SOFTWAREALA A:164 , TYR A:226 , SER A:303 , GLN A:304 , PHE A:376 , ETE A:527 , HOH A:570BINDING SITE FOR RESIDUE 250 A 517
29AF3SOFTWAREASP A:290 , LYS A:291 , TRP A:442 , PRO A:445 , ARG A:449 , HOH A:726 , HOH A:730BINDING SITE FOR RESIDUE ETE A 520
30AF4SOFTWAREGLY A:18 , LEU A:19 , VAL A:22 , HIS A:161 , ASN A:246 , GLN A:304 , LYS A:305 , VAL A:372 , SER A:374 , ALA A:377 , PRO A:378 , CYS A:379 , GLY A:380 , ADP A:500 , HOH A:533BINDING SITE FOR RESIDUE ETE A 521
31AF5SOFTWAREALA A:402 , ASP A:403 , VAL A:405 , SER A:406 , ASP A:407 , ASN A:412 , VAL A:422 , HOH A:720BINDING SITE FOR RESIDUE ETE A 522
32AF6SOFTWAREHIS A:86 , ASP A:89 , PHE A:450 , GLN A:454 , ALA A:457BINDING SITE FOR RESIDUE ETE A 523
33AF7SOFTWAREPHE A:127 , GLC A:506 , GLC A:507 , GLC A:510BINDING SITE FOR RESIDUE ETE A 524
34AF8SOFTWAREPHE A:127BINDING SITE FOR RESIDUE ETE A 525
35AF9SOFTWAREALA A:164 , TYR A:165 , GLN A:166 , GLY A:167 , MET A:168 , ETE A:527 , HOH A:578 , HOH A:637BINDING SITE FOR RESIDUE ETE A 526
36AG1SOFTWAREALA A:164 , TYR A:165 , THR A:302 , SER A:303 , GLC A:503 , 250 A:517 , ETE A:526 , HOH A:595BINDING SITE FOR RESIDUE ETE A 527
37AG2SOFTWAREPHE A:11 , LYS A:15 , ASP A:21 , ASP A:249 , ILE A:252 , TRP A:253 , GLU A:357 , HIS A:361 , HOH A:630 , HOH A:679BINDING SITE FOR RESIDUE ETE A 528
38AG3SOFTWARELEU A:410 , ARG A:444BINDING SITE FOR RESIDUE ETE A 529
39AG4SOFTWAREASP A:268 , ETE A:531 , HOH A:600BINDING SITE FOR RESIDUE ETE A 530
40BC2unknownILE A:186 , LYS A:199 , GLY A:230 , GLN A:234 , HOH A:580 , HOH A:655BINDING SITE FOR RESIDUE GLC A 511
41BC3unknownGLU A:190 , PHE A:191 , LYS A:199 , GLY A:227 , MET A:228 , GLU A:229 , GLY A:230 , LEU A:231 , HOH A:676BINDING SITE FOR RESIDUE GLC A 512
42BC4unknownILE A:186 , GLU A:190 , PHE A:191 , ASN A:192 , HOH A:676BINDING SITE FOR RESIDUE GLC A 513
43BC5unknownILE A:186BINDING SITE FOR RESIDUE GLC A 514
44BC6unknownHIS A:187BINDING SITE FOR RESIDUE GLC A 515
45BC7unknownHIS A:187BINDING SITE FOR RESIDUE BGC A 516
46BC8unknownARG A:300 , HOH A:629BINDING SITE FOR RESIDUE NA A 518
47BC9unknownTHR A:209 , ALA A:210 , TYR A:469BINDING SITE FOR RESIDUE NA A 519
48CC1unknownLYS A:15 , GLY A:17 , GLY A:18 , ASP A:21 , SER A:299 , ARG A:300 , LYS A:305 , LEU A:327 , GLY A:328 , GLY A:354 , TYR A:355 , HIS A:356 , LEU A:381 , THR A:382 , TYR A:385 , HOH A:533 , HOH A:609 , HOH A:629 , HOH A:634BINDING SITE FOR RESIDUE ADP A 500
49CC2unknownALA A:164 , TYR A:226 , SER A:303 , GLN A:304 , PHE A:376 , HOH A:570BINDING SITE FOR RESIDUE 250 A 517
50CC3unknownASP A:290 , LYS A:291 , TRP A:442 , PRO A:445 , ARG A:449 , HOH A:726 , HOH A:730BINDING SITE FOR RESIDUE ETE A 520
51CC4unknownGLY A:18 , LEU A:19 , HIS A:161 , ASN A:246 , GLN A:304 , LYS A:305 , SER A:374 , ALA A:377 , PRO A:378 , CYS A:379 , GLY A:380 , HOH A:533BINDING SITE FOR RESIDUE ETE A 521
52CC5unknownALA A:402 , ASP A:403 , SER A:406 , ASP A:407 , ASN A:412 , HOH A:720BINDING SITE FOR RESIDUE ETE A 522
53CC6unknownHIS A:86 , ASP A:89 , PHE A:450 , GLN A:454 , ALA A:457BINDING SITE FOR RESIDUE ETE A 523
54CC7unknownPHE A:127BINDING SITE FOR RESIDUE ETE A 524
55CC8unknownALA A:164 , TYR A:165 , GLN A:166 , GLY A:167 , MET A:168 , HOH A:578 , HOH A:637BINDING SITE FOR RESIDUE ETE A 526
56CC9unknownALA A:164 , TYR A:165 , THR A:302 , SER A:303 , HOH A:595BINDING SITE FOR RESIDUE ETE A 527
57DC1unknownPHE A:11 , LYS A:15 , ASP A:21 , ASP A:249 , ILE A:252 , TRP A:253 , GLU A:357 , HIS A:361 , HOH A:630 , HOH A:679BINDING SITE FOR RESIDUE ETE A 528
58DC2unknownLEU A:410 , ARG A:444BINDING SITE FOR RESIDUE ETE A 529
59DC3unknownASP A:268 , HOH A:600BINDING SITE FOR RESIDUE ETE A 530
60DC4unknownARG A:48 , ARG A:49BINDING SITE FOR RESIDUE ETE A 531
61DC5SOFTWAREARG A:48 , ARG A:49 , ETE A:530BINDING SITE FOR RESIDUE ETE A 531

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CX4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CX4)

(-) Exons   (0, 0)

(no "Exon" information available for 3CX4)

(-) 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:476
 aligned with GLGA_ECOLI | P0A6U8 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:476
                                    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      
           GLGA_ECOLI     1 MQVLHVCSEMFPLLKTGGLADVIGALPAAQIADGVDARVLLPAFPDIRRGVTDAQVVSRRDTFAGHITLLFGHYNGVGIYLIDAPHLYDRPGSPYHDTNLFAYTDNVLRFALLGWVGAEMASGLDPFWRPDVVHAHDWHAGLAPAYLAARGRPAKSVFTVHNLAYQGMFYAHHMNDIQLPWSFFNIHGLEFNGQISFLKAGLYYADHITAVSPTYAREITEPQFAYGMEGLLQQRHREGRLSGVLNGVDEKIWSPETDLLLASRYTRDTLEDKAENKRQLQIAMGLKVDDKVPLFAVVSRLTSQKGLDLVLEALPGLLEQGGQLALLGAGDPVLQEGFLAAAAEYPGQVGVQIGYHEAFSHRIMGGADVILVPSRFEPCGLTQLYGLKYGTLPLVRRTGGLADTVSDCSLENLADGVASGFVFEDSNAWSLLRAIRRAFVLWSRPSLWRFVQRQAMAMDFSWQVAAKSYRELYYRL 476
               SCOP domains d3cx4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3cx4A02 A:249-458 Glycogen Phosphorylase B;                                                                                                                                                                       ------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh...eeeeee......eeeeeeee..eeeeeeehhhhhh...............hhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhh....eeeeee.......eee.hhhhh...hhhhh.....ee..eeehhhhhhhhh.eeee.hhhhhhhh.hhhhhh.hhhhhhhhhhh..eee.........................hhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.eeee........hhhhhhhhhh.eeeee.hhhhhhhh...hhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cx4 A   1 MQVLHVCSEMFPLLKTGGLADVIGALPAAQIADGVDARVLLPAFPDIRRGVTDAQVVSRRDTFAGHITLLFGHYNGVGIYLIDAPHLYDRPGSPYHDTNLFAYTDNVLRFALLGWVGAEMASGLDPFWRPDVVHAHDWHAGLAPAYLAARGRPAKSVFTVHNLAYQGMFYAHHMNDIQLPWSFFNIHGLEFNGQISFLKAGLYYADHITAVSPTYAREITEPQFAYGMEGLLQQRHREGRLSGVLNGVDEKIWSPETDLLLASRYTRDTLEDKAENKRQLQIAMGLKVDDKVPLFAVVSRLTSQKGLDLVLEALPGLLEQGGQLALLGAGDPVLQEGFLAAAAEYPGQVGVQIGYHEAFSHRIMGGADVILVPSRFAPCGLTQLYGLKYGTLPLVRRTGGLADTVSDCSLENLADGVASGFVFEDSNAWSLLRAIRRAFVLWSRPSLWRFVQRQAMAMDFSWQVAAKSYRELYYRL 476
                                    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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CX4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLGA_ECOLI | P0A6U8)
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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        GLGA_ECOLI | P0A6U8: 2qzs 2r4t 2r4u 3cop 3d1j 3guh

(-) Related Entries Specified in the PDB File

3cop CRYSTAL STRUCTURE OF E.COLI GS MUTANT E377A IN COMPLEX WITH ADP AND ACCEPTOR ANALOGUE HEPPSO