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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GLUCURONIDASE FROM ACIDOBACTERIUM CAPSULATUM
 
Authors :  M. Momma, Z. Fujimoto, M. Michikawa, H. Ichinose, M. Yoshida, Y. Kotake Y. Tsumuraya, S. Kaneko
Date :  18 Jan 12  (Deposition) - 22 Feb 12  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (4x)
Keywords :  Tim Barrel, Greek-Key, Glycoside Hydrolase Family 79, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Michikawa, H. Ichinose, M. Momma, P. Biely, S. Jongkees, M. Yoshida T. Kotake, Y. Tsumuraya, S. G. Withers, Z. Fujimoto, S. Kaneko
Structural And Biochemical Characterization Of Glycoside Hydrolase Family 79 Beta-Glucuronidase From Acidobacterium Capsulatum
J. Biol. Chem. V. 287 14069 2012
PubMed-ID: 22367201  |  Reference-DOI: 10.1074/JBC.M112.346288

(-) Compounds

Molecule 1 - BETA-GLUCURONIDASE
    Chains: A
    EC Number: 3.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21GOLD (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ACP_2665
    Organism Scientific: ACIDOBACTERIUM CAPSULATUM
    Organism Taxid: 240015
    Strain: ATCC 51196

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:103 , GLY A:330 , TYR A:331 , GLY A:332 , GOL A:503 , HOH A:784 , HOH A:960BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWAREGLU A:45 , GLY A:79 , ASN A:80 , ASP A:105 , ASN A:172 , GLU A:173 , GLU A:287 , HIS A:327 , TYR A:334 , HOH A:961BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWARETYR A:331 , TRP A:333 , ARG A:348 , ARG A:425 , PO4 A:501 , HOH A:640 , HOH A:858BINDING SITE FOR RESIDUE GOL A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:214 -Pro A:215
2Gly A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VNY)

(-) 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:466
 aligned with C1F2K5_ACIC5 | C1F2K5 from UniProtKB/TrEMBL  Length:475

    Alignment length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   475        
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       | -      
         C1F2K5_ACIC5    18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGHSGQFVLHMRKASGALLEFA--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee.....eeeee.hhhhh.......hhhhhhhhhhhh...eeeeehhhhh.eee....hhhhh.................eeehhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh.eeeeeeeee........hhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhh...eeee.........eeee...eeeehhhhhhhhhhhhhh.eeeeeeeee.......eeeeeeee....eeeeeee......eeeeee.....eeeeeeee..........ee.....hhhhh......eeee.....eeeee...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vny A  18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGHSGQFVLHMRKASGALLEFAKLAAALQH 483
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477
   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 3VNY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VNY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (C1F2K5_ACIC5 | C1F2K5)
molecular function
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  3vny
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  3.2.1.31
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 Related Entries

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

UniProtKB/Swiss-Prot
        C1F2K5_ACIC5 | C1F2K5: 5g0m 5g0q 5l77
UniProtKB/TrEMBL
        C1F2K5_ACIC5 | C1F2K5: 3vnz 3vo0

(-) Related Entries Specified in the PDB File

3vnz 3vo0