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(-) Description

Title :  CRYSTAL STRUCTURE OF BPGH117_E303Q IN COMPLEX WITH NEOAGAROBIOSE
 
Authors :  J. H. Hehemann, L. Smyth, A. Yadav, D. J. Vocadlo, A. B. Boraston
Date :  21 Feb 12  (Deposition) - 14 Mar 12  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Marine Glycoside Hydrolase, Marine Polysaccharide Degradation, Marine Cazymes, Agar Metabolism, Seaweed Biofuels (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Hehemann, L. Smyth, A. Yadav, D. J. Vocadlo, A. B. Boraston
Analysis Of Keystone Enzyme In Agar Hydrolysis Provides Insight Into The Degradation (Of A Polysaccharide From) Red Seaweeds.
J. Biol. Chem. V. 287 13985 2012
PubMed-ID: 22393053  |  Reference-DOI: 10.1074/JBC.M112.345645

(-) Compounds

Molecule 1 - ANHYDRO-ALPHA-L-GALACTOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: BPGH117_E303Q, RESIDUES 22-402
    Mutation: YES
    Organism Scientific: BACTEROIDES PLEBEIUS
    Organism Taxid: 310297

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
147N2Ligand/IonNEOAGAROBIOSE
2ACT2Ligand/IonACETATE ION
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5EDO2Ligand/Ion1,2-ETHANEDIOL
6MG2Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:125 , TRP A:127 , THR A:165 , GLN A:180 , HIS A:244 , ASP A:245 , LYS A:260 , GLU A:262 , ARG A:273 , HIS A:302 , GLN A:303 , HOH A:2091 , HOH A:2092 , HOH A:2143 , HOH A:2259 , HOH A:2383 , HOH A:2424 , HOH A:2425 , HIS B:392BINDING SITE FOR RESIDUE 47N A1402
02AC2SOFTWARETYR A:186 , ASN A:192 , LYS A:242 , HIS A:244BINDING SITE FOR RESIDUE CA A1403
03AC3SOFTWARELYS A:191 , GLU A:215 , HOH A:2242 , HOH A:2426 , HOH A:2427BINDING SITE FOR RESIDUE EDO A1404
04AC4SOFTWAREMET A:339BINDING SITE FOR RESIDUE EDO A1405
05AC5SOFTWARELYS A:235 , HOH A:2295 , SER B:41BINDING SITE FOR RESIDUE ACT A1406
06AC6SOFTWAREHOH A:2095 , HOH A:2096 , HOH A:2097 , HOH A:2099 , HOH A:2324 , HOH A:4001BINDING SITE FOR RESIDUE MG A1407
07AC7SOFTWAREHIS A:392 , HOH A:2406 , ASP B:90 , TRP B:127 , THR B:165 , GLN B:180 , HIS B:244 , ASP B:245 , LYS B:260 , GLU B:262 , ARG B:273 , HIS B:302 , HOH B:2083 , HOH B:2084 , HOH B:2143 , HOH B:2352 , HOH B:2353BINDING SITE FOR RESIDUE 47N B1403
08AC8SOFTWARETYR B:186 , ASN B:192 , LYS B:242 , HIS B:244BINDING SITE FOR RESIDUE CL B1404
09AC9SOFTWAREPRO B:91 , HOH B:2087 , HOH B:2088 , HOH B:2089 , HOH B:2091 , HOH B:2290 , HOH B:4001BINDING SITE FOR RESIDUE MG B1405
10BC1SOFTWAREASP A:79 , HOH A:2071 , HOH A:2077 , HOH A:2082 , HOH B:2160BINDING SITE FOR RESIDUE ACT B1406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AK7)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:184 -Pro A:185
2Gly A:204 -Leu A:205
3Gly A:287 -Pro A:288
4Asn A:295 -Pro A:296
5Ser B:184 -Pro B:185
6Gly B:204 -Leu B:205
7Gly B:287 -Pro B:288
8Asn B:295 -Pro B:296

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AK7)

(-) Exons   (0, 0)

(no "Exon" information available for 4AK7)

(-) 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:369
 aligned with B5CY74_BACPM | B5CY74 from UniProtKB/TrEMBL  Length:402

    Alignment length:369
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392         
         B5CY74_BACPM    33 NYDERKADSLGIPKGNKLSAAMKRAMKWENHDNKWFFEYKMEPLKGDLAYEEGVVRRDPSAMLKIGDTYYVWYSKSYGPTQGFAGDIEKDKVFPWDRCDIWYATSKDGLTWKEQGIAVKRGEKGAYDDRSVFTPEVMEWKGKYYLCYQAVKSPYTVRVKNTIGMACADSPEGLWTKTDKPVLEPSDTGEWEGDEDNRFKVVSKGDFDSHKVHDPCIIPYNGKFYMYYKGERMGEEITWGGREIKHGVAIAENPMGPYVKSEYNPISNSGHEVCVWPYKGGIASLITTDGPEKNTLQWSPDGINFEIMSVVKGAPHAIGLNRSADAEKEPTEILRWGLTHIYNSSDYQSIMRFSTWTLQTHTAKGESKER 401
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh........hhhhhhhhh..........eeeeee.ee.......eeee.....eee..eeeeeeeeee.....................eeeeeee....eeeeeeeee...........eeeeeeeeee..eeeeeeeee..........eeeeeee.......ee............ee.........eee.......eeeeeeeeee..eeeeeeeee.....ee..ee..eeeeeee.......ee..............eeee..eeeeee........eeeee......eeeee........ee....hhhhh.hhhh.eeeeeee.....eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak7 A  33 NYDERKADSLGIPKGNKLSAAMKRAMKWENHDNKWFFEYKMEPLKGDLAYEEGVVRRDPSAMLKIGDTYYVWYSKSYGPTQGFAGDIEKDKVFPWDRCDIWYATSKDGLTWKEQGIAVKRGEKGAYDDRSVFTPEVMEWKGKYYLCYQAVKSPYTVRVKNTIGMACADSPEGLWTKTDKPVLEPSDTGEWEGDEDNRFKVVSKGDFDSHKVHDPCIIPYNGKFYMYYKGERMGEEITWGGREIKHGVAIAENPMGPYVKSEYNPISNSGHQVCVWPYKGGIASLITTDGPEKNTLQWSPDGINFEIMSVVKGAPHAIGLNRSADAEKEPTEILRWGLTHIYNSSDYQSIMRFSTWTLQTHTAKGESKER 401
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392         


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with B5CY74_BACPM | B5CY74 from UniProtKB/TrEMBL  Length:402

    Alignment length:373
                                    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   
         B5CY74_BACPM    30 DTQNYDERKADSLGIPKGNKLSAAMKRAMKWENHDNKWFFEYKMEPLKGDLAYEEGVVRRDPSAMLKIGDTYYVWYSKSYGPTQGFAGDIEKDKVFPWDRCDIWYATSKDGLTWKEQGIAVKRGEKGAYDDRSVFTPEVMEWKGKYYLCYQAVKSPYTVRVKNTIGMACADSPEGLWTKTDKPVLEPSDTGEWEGDEDNRFKVVSKGDFDSHKVHDPCIIPYNGKFYMYYKGERMGEEITWGGREIKHGVAIAENPMGPYVKSEYNPISNSGHEVCVWPYKGGIASLITTDGPEKNTLQWSPDGINFEIMSVVKGAPHAIGLNRSADAEKEPTEILRWGLTHIYNSSDYQSIMRFSTWTLQTHTAKGESKERK 402
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh........hhhhhhhhh..........eeeeee.ee.......eeee.....eee..eeeeeeeeee.....................eeeeeee....eeeeeeeee...........eeeeeeeeee..eeeeeeeee..........eeeeeee.......ee............ee.........eee.......eeeeeeeeee..eeeeeeeee.....ee..ee..eeeeeee.......ee..............eeee..eeeeee........eeeee......eeeee..............hhhhh.hhhh.eeeeeee.....eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ak7 B  30 DTQNYDERKADSLGIPKGNKLSAAMKRAMKWENHDNKWFFEYKMEPLKGDLAYEEGVVRRDPSAMLKIGDTYYVWYSKSYGPTQGFAGDIEKDKVFPWDRCDIWYATSKDGLTWKEQGIAVKRGEKGAYDDRSVFTPEVMEWKGKYYLCYQAVKSPYTVRVKNTIGMACADSPEGLWTKTDKPVLEPSDTGEWEGDEDNRFKVVSKGDFDSHKVHDPCIIPYNGKFYMYYKGERMGEEITWGGREIKHGVAIAENPMGPYVKSEYNPISNSGHQVCVWPYKGGIASLITTDGPEKNTLQWSPDGINFEIMSVVKGAPHAIGLNRSADAEKEPTEILRWGLTHIYNSSDYQSIMRFSTWTLQTHTAKGESKERK 402
                                    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
   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 4AK7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AK7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AK7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B5CY74_BACPM | B5CY74)
molecular function
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-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.

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 Related Entries

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

UniProtKB/TrEMBL
        B5CY74_BACPM | B5CY74: 4ak5 4ak6

(-) Related Entries Specified in the PDB File

4ak5 NATIVE CRYSTAL STRUCTURE OF BPGH117
4ak6 BPGH117_H302E MUTANT GLYCOSIDE HYDROLASE