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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCOGEN DEBRANCHING ENZYME TREX FROM SULFOLOBUS SOLFATARICUS
 
Authors :  H. -N. Song, S. -M. Yoon, H. Cha, K. -T. Park, E. -J. Woo
Date :  04 Feb 08  (Deposition) - 29 Jul 08  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydrolase, Glycosidase, Glycosyl Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. -J. Woo, S. Lee, H. Cha, J. -T. Park, S. -M. Yoon, H. -M. Song, K. -H. Par
Structural Insight Into The Bifunctional Mechanism Of The Glycogen-Debranching Enzyme Trex From The Archaeon Sulfolobus Solfataricus.
J. Biol. Chem. V. 283 28641 2008
PubMed-ID: 18703518  |  Reference-DOI: 10.1074/JBC.M802560200

(-) Compounds

Molecule 1 - GLYCOGEN OPERON PROTEIN GLGX
    Chains: A, B
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Other Details: DISULFIDE BOND BETWEEN A 254 AND A 261
    Synonym: GLYCOGEN DEBRANCHING ENZYME, TREX

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2VNC)

(-) Sites  (0, 0)

(no "Site" information available for 2VNC)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:254 -A:261
2A:505 -A:519
3B:254 -B:261
4B:505 -B:519

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Tyr A:18 -Pro A:19
2Ile A:128 -Gly A:129
3Lys A:165 -Gly A:166
4Asp A:645 -Glu A:646
5Glu A:646 -Ile A:647
6Glu A:717 -Leu A:718
7Asp B:9 -Arg B:10
8Tyr B:18 -Pro B:19
9Lys B:165 -Gly B:166
10Leu B:618 -Glu B:619
11Glu B:640 -Gly B:641
12Lys B:691 -Pro B:692
13Leu B:703 -Glu B:704

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VNC)

(-) 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:699
 aligned with P95868_SULSF | P95868 from UniProtKB/TrEMBL  Length:718

    Alignment length:710
                                    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       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718
         P95868_SULSF     9 DRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....eeeeeee.....eeeeeee.........eeeee.eee..eeeeeee......eeeeeee..eehhhhee.....................hhhhh.......hhhhh............ee.........hhhhhh....hhhhh.eeeehhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.................hhhhh.....hhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhh...........................hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhhhhh......eeee..................eeeehhhhhhhhhhhhhh..eehhhhhhhhh...........hhh.eee........hhhhhh......hhhhh......................hhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.....-----------.eeee..............ee.eeeeee...ee.........ee...eeeeee.....eeee....eeeeeee......hhhhheee...eeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vnc A   9 DRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYF-----------DVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
                                    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       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598 |       -   |   618       628       638       648       658       668       678       688       698       708       718
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         600         612                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:666
 aligned with P95868_SULSF | P95868 from UniProtKB/TrEMBL  Length:718

    Alignment length:709
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706         
         P95868_SULSF     7 TRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRR 715
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------CBM_48-2vncB03 B:19-110                                                                     --------------------------------------------------------------------------------------Alpha-amylase-2vncB05 B:197-554                                                                                                                                                                                                                                                                                                                                       --------------------------------------------             --------------------Alpha-amyl               ase_C-2vncB01 B:632-715                                     Pfam domains (1)
           Pfam domains (2) ------------CBM_48-2vncB04 B:19-110                                                                     --------------------------------------------------------------------------------------Alpha-amylase-2vncB06 B:197-554                                                                                                                                                                                                                                                                                                                                       --------------------------------------------             --------------------Alpha-amyl               ase_C-2vncB02 B:632-715                                     Pfam domains (2)
         Sec.struct. author ..............eeeee....eeeeeee.....eeeeeee.........eeeee.eee..eeeeeee......eeeeeee..eehhhhee..................................................ee.........hhhhhh..........eeeehhhhhhh...........hhhhhh.hhhhhhhhhhh..eeee........hhhhhh.................hhhhh.....hhhhhhhhhhhhhhhhhh.eeeeee...............hhhhhh......ee..eeeee.............hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh..hhhhhhhhhhhh......eeee..................eeee..hhhhhhhhhh.......hhhhhhhhh....---...hhh.eeee................--......................------......hhhhhhhhhhhhhh....eeeee...................................hhhhhhhhhhhhh.hhhhh...-------------....ee...ee...........eeeeee..---------------..eeeeee..............................----...........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vnc B   7 TRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDI---NNKTPFASINYVTSHDGFTLEDLVSYN--HNEANGFNNQDGMNENYSWNCG------DQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRER-------------DVTFYTLEGREVDEKTWSSPTQLVIFVLEG---------------DSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEE----GEKELEIEGRTALVYRR 715
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446     | 456       466       476     | 486       496       506      |516       526       536       546       556       566       576       586       596 |       -     | 616       626       636    |    -         -|      666       676       686       | -  |    706         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       452 456                       482  |                  506    513                                                                                  598           612                          641             657                                  694  699                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        485
   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  (0, 0)

(no "SCOP Domain" information available for 2VNC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P95868_SULSF | P95868)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004133    glycogen debranching enzyme activity    Catalysis of the cleavage of branch points in branched glycogen polymers.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0005980    glycogen catabolic process    The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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(no "Sites" information available for 2vnc)
 
  Cis Peptide Bonds
    Asp A:645 - Glu A:646   [ RasMol ]  
    Asp B:9 - Arg B:10   [ RasMol ]  
    Glu A:646 - Ile A:647   [ RasMol ]  
    Glu A:717 - Leu A:718   [ RasMol ]  
    Glu B:640 - Gly B:641   [ RasMol ]  
    Ile A:128 - Gly A:129   [ RasMol ]  
    Leu B:618 - Glu B:619   [ RasMol ]  
    Leu B:703 - Glu B:704   [ RasMol ]  
    Lys A:165 - Gly A:166   [ RasMol ]  
    Lys B:165 - Gly B:166   [ RasMol ]  
    Lys B:691 - Pro B:692   [ RasMol ]  
    Tyr A:18 - Pro A:19   [ RasMol ]  
    Tyr B:18 - Pro B:19   [ RasMol ]  
 
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  2vnc
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  P95868_SULSF | P95868
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 Related Entries

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

UniProtKB/TrEMBL
        P95868_SULSF | P95868: 2vr5 2vuy

(-) Related Entries Specified in the PDB File

2vnb CRYSTAL STRUCTURE OF GLYCOGEN DEBRANCHING ENZYME TREX FROM SULFOLOBUS SOLFATARIUS
2vr5 CRYSTAL STRUCTURE OF TREX FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH ACARBOSE INTERMEDIATE AND GLUCOSE
2vuy CRYSTAL STRUCTURE OF GLYCOGEN DEBRANCHING EXZYME TREX FROM SULFOLOBUS SOLFATARIUS