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(-) Description

Title :  THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH MSMSME
 
Authors :  A. J. Thompson, G. Speciale, J. Iglesias-Fernandez, Z. Hakki, T. Belz, A. Cartmell, R. J. Spears, J. Stepper, H. J. Gilbert, C. Rovira, S. J. Wi G. J. Davies
Date :  27 Oct 14  (Deposition) - 25 Mar 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, 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
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MAN2Ligand/IonALPHA-D-MANNOSE
3MSX2Ligand/Ion1,6-DIDEOXY-DITHIO-METHYL-ALPHA-D-MANNOSE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MAN1Ligand/IonALPHA-D-MANNOSE
3MSX1Ligand/Ion1,6-DIDEOXY-DITHIO-METHYL-ALPHA-D-MANNOSE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MAN1Ligand/IonALPHA-D-MANNOSE
3MSX1Ligand/Ion1,6-DIDEOXY-DITHIO-METHYL-ALPHA-D-MANNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:73 , ASP A:124 , TRP A:128 , CYS A:183 , MSX A:500 , HOH A:2185BINDING SITE FOR RESIDUE EDO A 510
2AC2SOFTWARETRP B:73 , ASP B:124 , TRP B:128 , CYS B:183 , MSX B:500 , HOH B:2221BINDING SITE FOR RESIDUE EDO B 510
3AC3SOFTWARETRP 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 , EDO A:510 , HOH A:2266 , HOH A:2267 , HOH A:2331 , HOH A:2343 , HOH A:2418 , HOH A:2492 , HOH A:2494 , HOH A:2495 , HOH A:2496BINDING SITE FOR POLY-SACCHARIDE RESIDUES MSX A 500 THROUGH MAN A 501
4AC4SOFTWARETRP 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 , EDO B:510 , HOH B:2300 , HOH B:2301 , HOH B:2354 , HOH B:2372 , HOH B:2534 , HOH B:2535 , HOH B:2536 , HOH B:2537 , HOH B:2538 , HOH B:2539BINDING SITE FOR POLY-SACCHARIDE RESIDUES MSX B 500 THROUGH MAN B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D4B)

(-) 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 4D4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D4B)

(-) Exons   (0, 0)

(no "Exon" information available for 4D4B)

(-) 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.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4b A  39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGQGTYESWSSAAAVQALNG 374
                                    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     ||361       371   
                                                                                                                                                                                                                                                                                                                                                     354|                
                                                                                                                                                                                                                                                                                                                                                      358                


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               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....................hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4b B  19 HHHHHSSSDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 374
                                  ||41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371   
                                 25|                                                                                                                                                                                                                                                                                                                                               
                                  39
   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 4D4B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D4B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D4B)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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        Q9Z4P9_BACCI | Q9Z4P9: 4boj 4bok 4d4a 4d4c 4d4d 5agd

(-) Related Entries Specified in the PDB File

4d4a STRUCTURE OF THE CATALYTIC DOMAIN (BCGH76) OF THE BACILLUS CIRCULANS GH76 ALPHA MANNANASE, AMAN6.
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
5agd AN INACTIVE (D125N) VARIANT OF THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH ALPHA-1,6-MANNOPENTAOSE