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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS CIRCULANS TN-31 AMAN6 IN COMPLEX WITH MANNOBIOSE
 
Authors :  A. Striebeck, D. M. F. Van Aalten
Date :  21 May 13  (Deposition) - 28 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Striebeck, V. S. Borodkin, A. T. Ferenbach, D. M. F. Van Aalten
The Structure Of B. Circulans Aman6 Defines The Fold And Mechanism Of The Gh-76 Mannoprotein Transglycosylases And Bacterial Mannosidases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-1,6-MANNANASE
    Atcc: 29101
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 35-375
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397
    Other Details: 6-O-ALPHA-D-MANNOPYRANOSYL-D-MANNOPYRANOSE
    Strain: TN-31
    Synonym: AMAN6

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MAN6Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:172 , ASN A:181 , CYS A:183 , ASP A:228 , ARG A:229 , ASP A:239 , THR A:241 , TYR A:243 , ASN A:292 , LEU A:295 , HOH A:2207 , HOH A:2208 , HOH A:2259 , HOH A:2271 , HOH A:2275 , HOH A:2319 , HOH A:2325 , HOH A:2374 , LYS B:58 , ASP B:104BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN A1375 THROUGH MAN A1376
2AC2SOFTWARELYS A:58 , ASP A:104 , HOH A:2027 , HOH A:2028 , TRP B:172 , ASN B:181 , CYS B:183 , ASP B:228 , ARG B:229 , THR B:241 , TYR B:243 , ASN B:292 , LEU B:295 , HOH B:2172 , HOH B:2173 , HOH B:2221 , HOH B:2224 , HOH B:2229 , HOH B:2275 , HOH B:2280 , HOH B:2344 , HOH B:2345BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN B1375 THROUGH MAN B1376
3AC3SOFTWARETRP C:172 , ASN C:181 , CYS C:183 , ASP C:228 , ARG C:229 , ASP C:239 , THR C:241 , TYR C:243 , ASN C:292 , LEU C:295 , HOH C:2191 , HOH C:2192 , HOH C:2238 , HOH C:2244 , HOH C:2248 , HOH C:2294 , HOH C:2300 , HOH C:2364 , HOH C:2365 , HOH C:2366BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN C1375 THROUGH MAN C1376

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BOJ)

(-) 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:336
 aligned with Q9Z4P9_BACCI | Q9Z4P9 from UniProtKB/TrEMBL  Length:589

    Alignment length:336
                                    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       358       368      
         Q9Z4P9_BACCI    39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 374
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...ee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4boj A  39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDAWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 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       358       368      


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with Q9Z4P9_BACCI | Q9Z4P9 from UniProtKB/TrEMBL  Length:589

    Alignment length:336
                                    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       358       368      
         Q9Z4P9_BACCI    39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 374
               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
                 4boj B  39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDAWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWA------TYESWSSAAAVQALNG 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   |     -|      368      
                                                                                                                                                                                                                                                                                                                                                   352    359               


Chain C from PDB  Type:PROTEIN  Length:344
 aligned with Q9Z4P9_BACCI | Q9Z4P9 from UniProtKB/TrEMBL  Length:589

    Alignment length:355
                                    30        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     
         Q9Z4P9_BACCI    21 MLGSMPGIGTSKAYAYTASDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNGI 375
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-----------..hhhhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4boj C  32 PLG-----------AYTASDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDAWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHRNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNGI 375
                              |      -    |   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     
                             34          35
   Legend:   → Mismatch (orange background)
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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 4BOJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9Z4P9_BACCI | Q9Z4P9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

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 Related Entries

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        Q9Z4P9_BACCI | Q9Z4P9: 4bok 4d4a 4d4b 4d4c 4d4d 5agd

(-) Related Entries Specified in the PDB File

4bok CRYSTAL STRUCTURE OF BACILLUS CIRCULANS TN-31 AMAN6 IN COMPLEX WITH MANNOBIOSE