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(-) Description

Title :  CRYSTAL STRUCTURE OF ENGINEERED BETA-GLUCOSIDASE FROM SOIL METAGENOME
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  22 Mar 08  (Deposition) - 07 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Bgl, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Nam, S. J. Kim, M. Y. Kim, J. H. Kim, Y. S. Yeo, C. M. Lee, H. K. Jun, K. Y. Hwang
Crystal Structure Of Engineered Beta-Glucosidase From A Soil Metagenome.
Proteins V. 73 788 2008
PubMed-ID: 18712828  |  Reference-DOI: 10.1002/PROT.22199
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Mutation: YES
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1NA22Ligand/IonSODIUM ION
2SRT1Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:60 , HOH A:489 , HOH A:570 , HOH A:579BINDING SITE FOR RESIDUE NA A 1
02AC2SOFTWAREPRO A:79 , HOH A:558 , HOH A:561 , HOH A:803BINDING SITE FOR RESIDUE NA A 2
03AC3SOFTWAREHOH A:819BINDING SITE FOR RESIDUE NA A 3
04AC4SOFTWARELYS A:83 , ASN A:84 , ASP A:86 , GLU A:444 , TYR A:446 , SER A:447BINDING SITE FOR RESIDUE NA A 4
05AC5SOFTWARESER A:87 , HOH A:512 , HOH A:734 , HOH A:792BINDING SITE FOR RESIDUE NA A 5
06AC6SOFTWAREARG A:106 , GLY A:109 , HOH A:674 , HOH A:726BINDING SITE FOR RESIDUE NA A 6
07AC7SOFTWAREASP A:167 , HOH A:507 , HOH A:559BINDING SITE FOR RESIDUE NA A 7
08AC8SOFTWAREGLN A:123 , ARG A:128 , GLU A:182 , HOH A:491BINDING SITE FOR RESIDUE NA A 8
09AC9SOFTWARETYR A:446 , PHE A:457 , HOH A:587 , HOH A:808BINDING SITE FOR RESIDUE NA A 9
10BC1SOFTWAREGLU A:143 , LYS A:147 , HOH A:809BINDING SITE FOR RESIDUE NA A 10
11BC2SOFTWARELEU A:172 , SER A:173 , ARG A:174 , ARG A:229 , TYR A:368BINDING SITE FOR RESIDUE NA A 12
12BC3SOFTWAREGLU A:168 , SER A:173 , GLU A:175 , SER A:176 , HOH A:497BINDING SITE FOR RESIDUE NA A 13
13BC4SOFTWAREGLN A:243 , HOH A:704BINDING SITE FOR RESIDUE NA A 14
14BC5SOFTWAREALA A:247 , ASP A:473BINDING SITE FOR RESIDUE NA A 15
15BC6SOFTWAREPHE A:217 , GLU A:441 , ALA A:443 , GLU A:444 , HOH A:640BINDING SITE FOR RESIDUE NA A 16
16BC7SOFTWAREILE A:82 , HOH A:561BINDING SITE FOR RESIDUE NA A 17
17BC8SOFTWAREASP A:393 , GLN A:406 , HOH A:839 , HOH A:848BINDING SITE FOR RESIDUE NA A 483
18BC9SOFTWAREGLN A:318 , HOH A:548 , HOH A:606 , HOH A:722BINDING SITE FOR RESIDUE NA A 485
19CC1SOFTWARETYR A:332 , THR A:356 , TRP A:360 , GLY A:389 , HOH A:502BINDING SITE FOR RESIDUE NA A 486
20CC2SOFTWARETHR A:356 , MET A:358 , TRP A:360 , ALA A:390 , ALA A:391 , PHE A:450BINDING SITE FOR RESIDUE NA A 487
21CC3SOFTWAREGLN A:57 , HIS A:158 , ASN A:202 , GLU A:203 , TYR A:332 , GLU A:387 , TRP A:434 , GLU A:441 , TRP A:442 , HOH A:672BINDING SITE FOR RESIDUE SRT A 488

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CMJ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:218 -Pro A:219
2Pro A:343 -Pro A:344
3Ser A:353 -Pro A:354
4Trp A:434 -Ser A:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CMJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CMJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3CMJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:441
 aligned with Q0GMU3_9BACT | Q0GMU3 from UniProtKB/TrEMBL  Length:485

    Alignment length:452
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479  
         Q0GMU3_9BACT    30 KKGHQMTEHELQPFPKGFLWGAATSSYQIEGAWNEDGKGESIWDRFTRIPGKIKNGDSGDVACDHYHRYEQDLDLMRQLGLKTYRFSIAWARIQPDSSRQINQRGLDFYRRLVEGLHKRDILPMATLYHWDLPQWVEDEGGWLSRESASRFAEYTHALVAALGDQIPLWVTHNEPMVTVWAGYHMGLFAPGLKDPTLGGRVAHHLLLSHGQALQAFRALSPAGSQMGITLNFNTIYPVSAEPADVEAARRMHSFQNELFLEPLIRGQYNQATLMAYPNLPEFIAPEDMQTISAPIDFLGVNYYNPMRVKSSPQPPGIEVVQVESPVTAMGWEIAPEGLYDLLMGITRTYGKLPIYITENGAAFDDQPDQSGQVNDPQRVGYFQGHIGAARRALADGVDLRGYYAWSLLDNFEWAEGYSKRFGIIYVDFETQQRTLKQSAQWYRDVIARNGLA 481
               SCOP domains d3           cmja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3c           mjA00 A:41-481 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------.....eeeee.hhhhhh..........hhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhh..hhhhhhh....eeeee....eeeee......eeee.............hhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cmj A  41 KK-----------FPEGFLWGAATSSYQIEGAWNEDGKGESIWDRFTRIPGKIKNGDSGDVACDHYHRYEQDLDLMRQLGLKTYRFSIAWARIQPDSSRQINQRGLDFYRRLVEGLHKRDILPMATLYHWDLPQWVEDEGGWLSRESASRFAEYTHALVAALGDQIPLWVTHNEPMVTVWAGYHMGLFAPGLKDPTLGGRVAHHLLLSHGQALQAFRALSPAGSQMGITLNFNTIYPVSAEPADVEAARRMHSFQNELFLEPLIRGQYNQATLMAYPNLPEFIAPEDMQTISAPIDFLGVNYYNPMRVKSSPQPPGIEVVQVESPVTAMGWEIAPEGLYDLLMGITRTYGKLPIYITENGAAFDDQPDQSGQVNDPQRVGYFQGHIGAARRALADGVDLRGYYAWSLLDNFEWAEGYSKRFGIIYVDFETQQRTLKQSAQWYRDVIANNGLE 481
                             |       -   |    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479  
                             |          43                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                            42
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CMJ)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0GMU3_9BACT | Q0GMU3)
molecular function
    GO:0008422    beta-glucosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0102483    scopolin beta-glucosidase activity    Catalysis of the reaction: H2O + scopolin <=> beta-D-glucose + scopoletin
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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