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(-) Description

Title :  STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-1,2-DIDEOXYMANNOSE
 
Authors :  M. Petricevic, L. F. Sobala, P. Z. Fernandes, L. Raich, A. J. Thompson, G. Bernardo-Seisdedos, O. Millet, S. Zhu, M. Sollogoub, C. Rovira, J. Barbero, G. J. Davies, S. J. Williams
Date :  07 Oct 16  (Deposition) - 11 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym./Biol. Unit :  A
Keywords :  Endomannanase, Endomannosidase, Gh99, N-Glycosylation, Glycosylation, Inhibitor, Inhibition, Shape, Charge, Mannobiose, Mannose, Glycobiology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Petricevic, L. F. Sobala, P. Z. Fernandes, L. Raich, A. J. Thompson, G. Bernardo-Seisdedos, O. Millet, S. Zhu, M. Sollogoub, J. Jimenez-Barbero, C. Rovira, G. J. Davies, S. J. Williams
Contribution Of Shape And Charge To The Inhibition Of A Family Gh99 Endo-Alpha-1, 2-Mannanase.
J. Am. Chem. Soc. V. 139 1089 2017
PubMed-ID: 27992199  |  Reference-DOI: 10.1021/JACS.6B10075

(-) Compounds

Molecule 1 - GLYCOSYL HYDROLASE FAMILY 71
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: BXY_34140
    Organism Scientific: BACTEROIDES XYLANISOLVENS XB1A
    Organism Taxid: 657309

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
17D11Ligand/Ion(2~{R},3~{S},4~{R})-2-(HYDROXYMETHYL)OXANE-3,4-DIOL
2ACT1Ligand/IonACETATE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:151 , CYS A:152 , PHE A:153 , PHE A:183 , TYR A:184 , PRO A:190 , LEU A:191 , PHE A:192 , HOH A:599 , HOH A:619binding site for residue EDO A 401
2AC2SOFTWAREPHE A:253 , ALA A:254 , ALA A:255 , PHE A:258 , TYR A:289 , VAL A:301 , HOH A:522 , HOH A:747 , HOH A:749 , HOH A:787 , HOH A:820binding site for residue EDO A 402
3AC3SOFTWARELYS A:207 , SER A:214 , THR A:306 , GLN A:309 , TYR A:310 , HOH A:612binding site for residue ACT A 403
4AC4SOFTWARETYR A:46 , HIS A:60 , HIS A:63 , TRP A:126 , HIS A:154 , GLU A:156 , TYR A:195 , TYR A:252 , ILE A:294 , ARG A:295 , GLU A:333 , HIS A:335 , GLU A:336 , HOH A:611 , HOH A:615 , HOH A:722 , HOH A:786binding site for Poly-Saccharide residues MAN A 404 through 7D1 A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M17)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:329 -Ser A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M17)

(-) Exons   (0, 0)

(no "Exon" information available for 5M17)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee.....hhhhhh.....eee..............eee....................hhhhhhhhhhhhhhhheeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhh............eeee.hhhhhhhhhhhhhhh..............eeeee...hhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh..eee.ee............hhhhh..hhhhhhhhhhhhhhhhh....eee....hhhhh........................hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m17 A  31 NNLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTIPGTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQDETEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNHPAFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLWTSSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKIFIPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITSFNEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK 379
                                    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
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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 5M17)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M17)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M17)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr A:329 - Ser A:330   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        D6D1V7_9BACE | D6D1V7: 4ad1 4ad2 4ad3 4ad4 4ad5 4utf 4v27 4v28 5lyr 5m03 5m3w 5m5d 5mc8 5mel

(-) Related Entries Specified in the PDB File

4ad1 4AD1 CONTAINS THE SAME PROTEIN (APO).
4ad2 4AD2 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- ISOFAGOMINE.
4ad3 4AD3 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- DEOXYMANNOJIRIMYCIN.
4ad4 4AD4 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- ISOFAGOMINE AND ALPHA-1,2- MANNOBIOSE.
4ad5 4AD5 CONTAINS THE SAME PROTEIN IN COMPLEX WITH GLUCOSE-1,3- DEOXYMANNOJIRIMYCIN AND ALPHA-1,2-MANNOBIOSE.
4utf 4UTF CONTAINS THE SAME PROTEIN IN COMPLEX WITH MANNOSE-ALPHA-1,3- ISOFAGOMINE AND ALPHA- 1,2-MANNOBIOSE.
4v27 4V27 CONTAINS THE SAME PROTEIN IN COMPLEX WITH MANNOSE-ALPHA-1,3- ISOFAGOMINE.
4v28 4V28 CONTAINS AN E333Q VARIANT OF THE SAME PROTEIN WITH IN COMPLEX IN COMPLEX WITH MAN-MAN-METHYLUMBELLIFERONE.