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(-) Description

Title :  CRYSTAL STRUCTURE OF TREX FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH ACARBOSE INTERMEDIATE AND GLUCOSE
 
Authors :  H. -N. Song, S. -M. Yoon, S. -J. Lee, H. -J. Cha, K. -H. Park, E. -J. Woo
Date :  26 Mar 08  (Deposition) - 29 Jul 08  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hydrolase, Glycosidase, Glycosyl Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Woo, S. Lee, H. Cha, J. Park, S. Yoon, H. Song, K. Park
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, A 505 AND A 519, B 254 AND B 261, B 505 AND B 519
    Synonym: TREX, GLYCOGEN DEBRANCHING ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1A162Ligand/Ion4-O-(4,6-DIDEOXY-4-{[(1S,2S,3S,4R,5S)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}-ALPHA-D-GLUCOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
2GLC4Ligand/IonALPHA-D-GLUCOSE
3GOL1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1A166Ligand/Ion4-O-(4,6-DIDEOXY-4-{[(1S,2S,3S,4R,5S)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}-ALPHA-D-GLUCOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
2GLC12Ligand/IonALPHA-D-GLUCOSE
3GOL3Ligand/IonGLYCEROL
4SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:408 , LYS A:423 , HOH A:2210 , ASP B:130 , GLN B:131BINDING SITE FOR RESIDUE GLC A1719
2AC2SOFTWAREGLC A:1721 , TYR B:408BINDING SITE FOR RESIDUE GLC B1719
3AC3SOFTWARETRP A:401 , VAL A:403 , TYR A:408 , MET A:497 , HOH A:2211 , GLN B:131BINDING SITE FOR RESIDUE GLC A1720
4AC4SOFTWARETRP B:401 , ASP B:402 , VAL B:403 , GLC B:1719BINDING SITE FOR RESIDUE GLC A1721
5AC5SOFTWAREGLN A:230 , TRP A:242 , TYR A:244 , HIS A:291 , GLY A:328 , ASP A:363 , GLU A:399 , HIS A:470 , ASP A:471 , PHE A:491 , ASP A:495 , ASN A:555 , HOH A:2212BINDING SITE FOR RESIDUE A16 A1722
6AC6SOFTWAREGLN B:230 , PHE B:232 , TRP B:242 , TYR B:244 , HIS B:291 , GLY B:328 , ASP B:363 , GLU B:399 , HIS B:470 , ASP B:471 , ASP B:495 , ASN B:555BINDING SITE FOR RESIDUE A16 B1720
7AC7SOFTWAREARG A:6 , THR A:7 , ARG A:8 , LYS A:63 , HOH A:2021BINDING SITE FOR RESIDUE SO4 A1723
8AC8SOFTWAREPRO A:154 , PHE A:156 , TRP A:158 , LYS A:270 , GLU A:354 , HOH A:2213BINDING SITE FOR RESIDUE GOL A1724

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:18 -Pro A:19
2Tyr B:18 -Pro B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VR5)

(-) Exons   (0, 0)

(no "Exon" information available for 2VR5)

(-) 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:715
 aligned with P95868_SULSF | P95868 from UniProtKB/TrEMBL  Length:718

    Alignment length:715
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713     
         P95868_SULSF     4 FFRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeehhh.eeeeeee.....eeeeee..........eeeee.ee...eeeeeee......eeeeeee...............................hhhhh........................ee.........hhhhhh..........eeee..................hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.................hhhhh.....hhhhhhhhhhhhhhhh...eeeeee...............hhhhhhh...........................hhhhhhhhhhhhhhhhhh....eeee.hhhhhh.........hhhhhhhhhh.hhhhheeee..................eeeehhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhh.hhh.eee........hhhhhh......hhhhh......................hhhhhhhhhhhhhhhhhhhh....eeeee.............................hhhhhhhhhhhhhhhhhhhhhhhhh.................eeee..............ee.eeeeeee.hhh.............eeeeeee.....eeee....eeeeeee.................eeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vr5 A   4 FFRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713     


Chain B from PDB  Type:PROTEIN  Length:714
 aligned with P95868_SULSF | P95868 from UniProtKB/TrEMBL  Length:718

    Alignment length:714
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714    
         P95868_SULSF     5 FRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------CBM_48-2vr5B03 B:19-110                                                                     --------------------------------------------------------------------------------------Alpha-amylase-2vr5B05 B:197-554                                                                                                                                                                                                                                                                                                                                       -----------------------------------------------------------------------------Alpha-amylase_C-2vr5B01 B:632-716                                                    -- Pfam domains (1)
           Pfam domains (2) --------------CBM_48-2vr5B04 B:19-110                                                                     --------------------------------------------------------------------------------------Alpha-amylase-2vr5B06 B:197-554                                                                                                                                                                                                                                                                                                                                       -----------------------------------------------------------------------------Alpha-amylase_C-2vr5B02 B:632-716                                                    -- Pfam domains (2)
         Sec.struct. author ................eeeeehhh.eeeeeee.....eeeeeee.........eeee.......eeeeeee......eeeeeee..ee....ee..............ee.....hhhhh.......hhhhh.....hhhhh.eee...................hhhhh.eeeehhhhhhhh..........hhhhhhhhhhhhhhhhhh..eeee........hhhhhh.................hhhhh.....hhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhh....eeee.hhhhhh.........hhhhhhhhhh......eeee..................eeeehhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhh....hhh.eee........hhhhhh......hhhhh......................hhhhhhhhhhhhhhhhhhhh....eeeee.............................hhhhhhhhhhhhhhhhhhh.......................eeee........hhhhhhee.eeeeee.hhhh..............eeeeee.....eeee....eeeeeee......hhhh.eee...eeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vr5 B   5 FRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQKYPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKVLIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINPYFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLASEQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPECRYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSFRGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTEMHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVGQGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYLGNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWNCGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNNNAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKKLFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERIADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELEIEGRTALVYRRIEL 718
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2VR5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VR5)

(-) 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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  2vr5
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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: 2vnc 2vuy

(-) Related Entries Specified in the PDB File

2vnc CRYSTAL STRUCTURE OF GLYCOGEN DEBRANCHING ENZYME TREX FROM SULFOLOBUS SOLFATARICUS
2vuy CRYSTAL STRUCTURE OF GLYCOGEN DEBRANCHING EXZYME TREX FROM SULFOLOBUS SOLFATARIUS