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(-) Description

Title :  AN INACTIVE (D125N) VARIANT OF THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH ALPHA-1,6-MANNOPENTAOSE
 
Authors :  A. J. Thompson, G. Speciale, J. Iglesias-Fernandez, Z. Hakki, T. Belz, A. Cartmell, R. J. Spears, E. Chandler, M. J. Temple, J. Stepper, H. J. G C. Rovira, S. J. Williams, G. J. Davies
Date :  29 Jan 15  (Deposition) - 25 Mar 15  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Alpha-Mannanase, Mannanase, Glycoside Hydrolase, Gh76, Cazy, Mannan, Enzyme-Carbohydrate Interaction, Glycosidase Inhibition, Quantum Mechanics, Transition State (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Thompson, G. Speciale, J. Iglesias-Fernandez, Z. Hakki, T. Belz A. Cartmell, R. J. Spears, E. Chandler, M. J. Temple, J. Stepper, H. J. Gilbert, C. Rovira, S. J. Williams, G. J. Davies
Evidence For A Boat Conformation At The Transition State Of Gh76 Alpha-1, 6-Mannanases- Key Enzymes In Bacterial And Fungal Mannoprotein Metabolism
Angew. Chem. Int. Ed. Engl. V. 54 5378 2015
PubMed-ID: 25772148  |  Reference-DOI: 10.1002/ANIE.201410502

(-) Compounds

Molecule 1 - ALPHA-1,6-MANNANASE
    Atcc: 29101
    Chains: A, B
    EC Number: 3.2.1.101
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Variant: TUNER
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 35-375
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397
    Strain: TN31

 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  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN10Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN5Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN5Ligand/IonALPHA-D-MANNOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , TRP A:73 , PHE A:122 , ASP A:124 , ASN A:125 , TRP A:128 , TRP A:172 , ASN A:181 , CYS A:183 , ASP A:228 , ARG A:229 , ASP A:239 , THR A:241 , TYR A:243 , ASP A:294 , LEU A:295 , HOH A:2070 , HOH A:2291 , HOH A:2292 , HOH A:2350 , HOH A:2362 , HOH A:2366 , HOH A:2367 , HOH A:2505 , HOH A:2507 , HOH A:2508 , HOH A:2509 , HOH A:2511Binding site for Poly-Saccharide residues MAN A 500A through MAN A 504
2AC2SOFTWAREASP A:71 , TRP A:73 , PHE A:122 , ASP A:124 , ASN A:125 , TRP A:128 , TRP A:172 , ASN A:181 , CYS A:183 , ASP A:228 , ARG A:229 , ASP A:239 , THR A:241 , TYR A:243 , ASP A:294 , LEU A:295 , HOH A:2070 , HOH A:2291 , HOH A:2292 , HOH A:2350 , HOH A:2362 , HOH A:2366 , HOH A:2367 , HOH A:2505 , HOH A:2507 , HOH A:2508 , HOH A:2509 , HOH A:2511 , ASP B:71 , TRP B:73 , PHE B:122 , ASP B:124 , ASN B:125 , TRP B:128 , TRP B:172 , ASN B:181 , CYS B:183 , ASP B:228 , ARG B:229 , ASP B:239 , THR B:241 , TYR B:243 , ASP B:294 , LEU B:295 , HOH B:2108 , HOH B:2290 , HOH B:2291 , HOH B:2343 , HOH B:2358 , HOH B:2361 , HOH B:2362 , HOH B:2517 , HOH B:2519 , HOH B:2520 , HOH B:2521 , HOH B:2522 , HOH B:2523Binding site for Poly-Saccharide residues MAN B 500A through MAN B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:290 -Pro A:291
2Ser B:24 -Ser B:25
3Gly B:290 -Pro B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AGD)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agd A  39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDNIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGGTYESWSSAAAVQALNGI 375
                                    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    || 362       372   
                                                                                                                                                                                                                                                                                                                                                    353|                 
                                                                                                                                                                                                                                                                                                                                                     358                 


Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agd B  19 HHHHHSSASDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDNIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 374
                                  ||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    
                                 25|                                                                                                                                                                                                                                                                                                                                                
                                  38
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  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 5AGD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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        Q9Z4P9_BACCI | Q9Z4P9: 4boj 4bok 4d4a 4d4b 4d4c 4d4d

(-) Related Entries Specified in the PDB File

4d4a STRUCTURE OF THE CATALYTIC DOMAIN (BCGH76) OF THE BACILLUS CIRCULANS GH76 ALPHA MANNANASE, AMAN6.
4d4b THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH MSMSME
4d4c THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH 1,6-MANDMJ
4d4d THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH 1,6-MANIFG