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(-) Description

Title :  STRUCTURE OF GH36 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN A COVALENT COMPLEX WITH A CYCLOPROPYL CARBASUGAR.
 
Authors :  R. Pengelly, T. Gloster
Date :  07 Oct 16  (Deposition) - 09 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Galactosidase, Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Adamson, R. J. Pengelly, S. Shamsi Kazem Abadi, S. Chakladar, J. Draper, R. Britton, T. M. Gloster, A. J. Bennet
Structural Snapshots For Mechanism-Based Inactivation Of A Glycoside Hydrolase By Cyclopropyl Carbasugars.
Angew. Chem. Int. Ed. Engl. V. 55 14978 2016
PubMed-ID: 27783466  |  Reference-DOI: 10.1002/ANIE.201607431

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GALA
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
17D81Ligand/Ion(1~{R},2~{S},3~{S},4~{S},6~{R})-4-FLUORANYL-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3-DIOL
2EDO12Ligand/Ion1,2-ETHANEDIOL
3SO46Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:-3 , SER A:-4 , MET A:-2 , GLY A:-5 , LYS A:111 , ASN A:290 , TRP A:291 , ASN A:292 , HOH A:806 , HOH A:917binding site for residue SO4 A 601
02AC2SOFTWARELYS A:302 , ASP A:303 , GLU A:304 , LYS A:339binding site for residue SO4 A 602
03AC3SOFTWAREARG A:9 , TRP A:392 , GLY A:393 , GLU A:394 , HOH A:760 , HOH A:847binding site for residue SO4 A 603
04AC4SOFTWAREGLU A:434 , LYS A:435 , THR A:436binding site for residue SO4 A 604
05AC5SOFTWAREARG A:349 , GLU A:353 , HOH A:702 , HOH A:722 , HOH A:748binding site for residue SO4 A 605
06AC6SOFTWAREPHE A:143 , ASP A:144 , ASP A:145 , HOH A:733binding site for residue SO4 A 606
07AC7SOFTWARESER A:-4 , TRP A:65 , TRP A:190 , TYR A:191 , ASP A:220 , ASP A:221 , TRP A:257 , LYS A:325 , ASP A:327 , PHE A:328 , CYS A:368 , ARG A:383 , ASP A:387binding site for residue 7D8 A 607
08AC8SOFTWAREARG A:-6 , ASP A:387 , GLY A:400 , PRO A:402 , EDO A:609binding site for residue EDO A 608
09AC9SOFTWAREARG A:-6 , TRP A:65 , THR A:88 , GLY A:400 , EDO A:608 , EDO A:612binding site for residue EDO A 609
10AD1SOFTWAREALA A:-1 , PRO A:402 , HOH A:761 , HOH A:772 , HOH A:802 , HOH A:822binding site for residue EDO A 610
11AD2SOFTWARELYS A:181 , HIS A:182binding site for residue EDO A 611
12AD3SOFTWAREGLN A:63 , TRP A:65 , GLY A:66 , THR A:88 , ASN A:399 , EDO A:609 , EDO A:616 , HOH A:898binding site for residue EDO A 612
13AD4SOFTWARELYS A:357 , ARG A:496 , VAL A:512 , ASP A:514 , GLU A:519 , HOH A:701binding site for residue EDO A 613
14AD5SOFTWARESER A:-12 , HIS A:-13 , ARG A:405 , HOH A:764 , HOH A:843 , HOH A:870binding site for residue EDO A 614
15AD6SOFTWARELYS A:28 , ILE A:29 , HIS A:30 , LEU A:31 , HOH A:804 , HOH A:819binding site for residue EDO A 615
16AD7SOFTWAREARG A:-6 , ILE A:81 , ASP A:82 , THR A:88 , EDO A:612 , HOH A:876 , HOH A:936binding site for residue EDO A 616
17AD8SOFTWAREPRO A:184 , ARG A:322 , ASP A:362binding site for residue EDO A 617
18AD9SOFTWAREGLY A:235binding site for residue EDO A 618
19AE1SOFTWAREARG A:45 , ASN A:99 , GLU A:128 , TYR A:135 , HOH A:785binding site for residue EDO A 619

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M1I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M1I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M1I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M1I)

(-) Exons   (0, 0)

(no "Exon" information available for 5M1I)

(-) 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:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh.ee..ee...eeeeee...eeeeeeeeee..eeeeeeeeee...eeeeeeee...eeeee.......eeeee............hhhhhh.hhhhhh...eee.eeee..eeeee......eeeeeee..eeeeeee.....eeeeee...eeeee..hhhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhh.ee..ee.eeeee..eeeee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhh........hhhhhhhhhhhhhhhhhh...eeee....hhhhh....eee...................hhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeee........eeeeeeeee..eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1i A -13 HSSGLVPRGSHMASMEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPGRLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMAKVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKKIYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKKNITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPDTAPFWGEHIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKELYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSEDLRYEIVSSGTLSGNVKIVVDLNSREYHLEKE 525
                                    -4         6        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
   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 5M1I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M1I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M1I)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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        AGAL_THEMA | G4FEF4: 1zy9 5m0x 5m12 5m16

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