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(-) Description

Title :  SELENOMETHIONINE DERIVATIVE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES THETAIOTAOMICRON
 
Authors :  A. J. Thompson, R. J. Williams, Z. Hakki, D. S. Alonzi, T. Wennekes, T. M. K. Songsrirote, J. E. Thomas-Oates, T. M. Wrodnigg, J. Spreitz, A. E. S T. D. Butters, S. J. Williams, G. J. Davies
Date :  21 Dec 11  (Deposition) - 01 Feb 12  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Endomannosidase, Glycoside Hydrolase, Cazy, Enzyme- Carbohydrate Interaction, Mannose, Glycosidase Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Thompson, R. J. Williams, Z. Hakki, D. S. Alonzi, T. Wennekes, T. M. Gloster, K. Songsrirote, J. E. Thomas-Oates, T. M. Wrodnigg, J. Spreitz, A. E. Stutz, T. D. Butters, S. J. Williams, G. J. Davies
Structural And Mechanistic Insight Into N-Glycan Processing By Endo-Alpha-Mannosidase.
Proc. Natl. Acad. Sci. Usa V. 109 781 2012
PubMed-ID: 22219371  |  Reference-DOI: 10.1073/PNAS.1111482109

(-) Compounds

Molecule 1 - ENDO-ALPHA-MANNOSIDASE
    Atcc: 29148
    Chains: A, B
    EC Number: 3.2.1.130
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL7Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL3Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL4Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:73 , GLY A:74 , HIS B:64 , GOL B:1380 , HOH B:2030 , HOH B:2223 , HOH B:2261BINDING SITE FOR RESIDUE GOL B 1378
2AC2SOFTWARELEU A:229 , PHE A:254 , THR A:255 , HOH A:2201 , HOH A:2242 , HIS B:72 , HOH B:2043 , HOH B:2228 , HOH B:2296BINDING SITE FOR RESIDUE GOL B 1379
3AC3SOFTWAREHIS A:72 , HOH A:2053 , HOH A:2280 , HOH A:2348 , HOH A:2349 , LEU B:229 , PHE B:254BINDING SITE FOR RESIDUE GOL A 1378
4AC4SOFTWAREASP A:75 , TRP B:49 , HIS B:61 , TRP B:125 , GOL B:1378BINDING SITE FOR RESIDUE GOL B 1380
5AC5SOFTWAREHIS A:61 , HOH A:2352 , HOH A:2353 , ASP B:75BINDING SITE FOR RESIDUE GOL A 1379
6AC6SOFTWARELYS B:60 , HIS B:61 , MSE B:63 , HIS B:64 , PRO B:65 , HOH B:2031 , HOH B:2297BINDING SITE FOR RESIDUE GOL B 1381
7AC7SOFTWARELYS A:60 , HIS A:61 , MSE A:63 , HIS A:64 , PRO A:65 , HOH A:2030 , HOH A:2036 , HOH A:2354BINDING SITE FOR RESIDUE GOL A 1380
8AC8SOFTWARESER A:73 , HOH A:2059 , TYR B:47 , HIS B:152 , GLU B:154 , TYR B:193BINDING SITE FOR RESIDUE FMT B 1382
9AC9SOFTWARETYR A:47 , HIS A:152 , GLU A:154 , TYR A:193 , SER B:73BINDING SITE FOR RESIDUE FMT A 1381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ACY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:325 -Ser A:326
2Lys A:353 -Pro A:354
3Thr B:325 -Ser B:326
4Lys B:353 -Pro B:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ACY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ACY)

(-) Exons   (0, 0)

(no "Exon" information available for 4ACY)

(-) 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:341
 aligned with Q8A109_BACTN | Q8A109 from UniProtKB/TrEMBL  Length:382

    Alignment length:341
                                    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 
         Q8A109_BACTN    37 TLDDHTISFYYNWYGNPSVDGEMKHWMHPIALAPGHSGDVGAISGLNDDIACNFYPELGTYSSNDPEIIRKHIRMHIKANVGVLSVTWWGESDYGNQSVSLLLDEAAKVGAKVCFHIEPFNGRSPQTVRENIQYIVDTYGDHPAFYRTHGKPLFFIYDSYLIKPAEWAKLFAAGGEISVRNTKYDGLFIGLTLKESELPDIETACMDGFYTYFAATGFTNASTPANWKSMQQWAKAHNKLFIPSVGPGYIDTRIRPWNGSTTRDRENGKYYDDMYKAAIESGASYISITSFNEWHEGTQIEPAVSKKCDAFEYLDYKPLADDYYLIRTAYWVDEFRKARSA 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhh......eee..........eee.....................hhhhhhhhhhhhhhhheeeeeeeehhhhhh.hhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhh............eeee.hhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhh...eee............hhhhhhhhhhhhhhh..eee.ee............hhhhh..hhhhhhhhhhhhhhhhh....eee....hhhhh........................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4acy A  37 TLDDHTISFYYNWYGNPSVDGEmKHWmHPIALAPGHSGDVGAISGLNDDIACNFYPELGTYSSNDPEIIRKHIRmHIKANVGVLSVTWWGESDYGNQSVSLLLDEAAKVGAKVCFHIEPFNGRSPQTVRENIQYIVDTYGDHPAFYRTHGKPLFFIYDSYLIKPAEWAKLFAAGGEISVRNTKYDGLFIGLTLKESELPDIETACmDGFYTYFAATGFTNASTPANWKSmQQWAKAHNKLFIPSVGPGYIDTRIRPWNGSTTRDRENGKYYDDmYKAAIESGASYISITSFNEWHEGTQIEPAVSKKCDAFEYLDYKPLADDYYLIRTAYWVDEFRKARSA 377
                                    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 
                                                 59-MSE                                             111-MSE                                                                                                                            242-MSE                 266-MSE                                     310-MSE                                                               
                                                     63-MSE                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with Q8A109_BACTN | Q8A109 from UniProtKB/TrEMBL  Length:382

    Alignment length:341
                                    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 
         Q8A109_BACTN    37 TLDDHTISFYYNWYGNPSVDGEMKHWMHPIALAPGHSGDVGAISGLNDDIACNFYPELGTYSSNDPEIIRKHIRMHIKANVGVLSVTWWGESDYGNQSVSLLLDEAAKVGAKVCFHIEPFNGRSPQTVRENIQYIVDTYGDHPAFYRTHGKPLFFIYDSYLIKPAEWAKLFAAGGEISVRNTKYDGLFIGLTLKESELPDIETACMDGFYTYFAATGFTNASTPANWKSMQQWAKAHNKLFIPSVGPGYIDTRIRPWNGSTTRDRENGKYYDDMYKAAIESGASYISITSFNEWHEGTQIEPAVSKKCDAFEYLDYKPLADDYYLIRTAYWVDEFRKARSA 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhh......eee..........eee...........ee........hhhhhhhhhhhhhhhheeeeeeeehhhhhh.hhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhh............eeee.hhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhh...eee............hhhhhhhhhhhhhhh..eee.ee............hhhhh..hhhhhhhhhhhhhhhhhh...eee....hhhhh.....ee..ee..ee.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4acy B  37 TLDDHTISFYYNWYGNPSVDGEmKHWmHPIALAPGHSGDVGAISGLNDDIACNFYPELGTYSSNDPEIIRKHIRmHIKANVGVLSVTWWGESDYGNQSVSLLLDEAAKVGAKVCFHIEPFNGRSPQTVRENIQYIVDTYGDHPAFYRTHGKPLFFIYDSYLIKPAEWAKLFAAGGEISVRNTKYDGLFIGLTLKESELPDIETACmDGFYTYFAATGFTNASTPANWKSmQQWAKAHNKLFIPSVGPGYIDTRIRPWNGSTTRDRENGKYYDDmYKAAIESGASYISITSFNEWHEGTQIEPAVSKKCDAFEYLDYKPLADDYYLIRTAYWVDEFRKARSA 377
                                    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 
                                                 59-MSE                                             111-MSE                                                                                                                            242-MSE                 266-MSE                                     310-MSE                                                               
                                                     63-MSE
   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 4ACY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ACY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ACY)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4ACY)

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 Related Entries

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

UniProtKB/TrEMBL
        Q8A109_BACTN | Q8A109: 4acz 4ad0

(-) Related Entries Specified in the PDB File

4acz STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES THETAIOTAOMICRON
4ad0 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTERIODES THETAIOTAOMICRON IN COMPLEX WITH BIS-TRIS- PROPANE
4ad1 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES XYLANISOLVENS
4ad2 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3- ISOFAGOMINE
4ad3 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3- DEOXYMANNOJIRIMYCIN
4ad4 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3- ISOFAGOMINE AND ALPHA-1, 2-MANNOBIOSE
4ad5 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3- DEOXYMANNOJIRIMYCIN AND ALPHA-1,2-MANNOBIOSE