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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL ALPHA-GALACTOSIDASE FROM PEDOBACTER SALTANS
 
Authors :  T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka
Date :  17 Jan 15  (Deposition) - 20 May 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Tim-Barrel, Gh31 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka
Structural And Biochemical Characterization Of Novel Bacterial Alpha-Galactosidases Belonging To Glycoside Hydrolase Family 31
Biochem. J. V. 469 145 2015
PubMed-ID: 25942325  |  Reference-DOI: 10.1042/BJ20150261

(-) Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PEDOBACTER SALTANS
    Organism Taxid: 151895
    Strain: NBRC 100064

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:266 , TRP A:305 , LYS A:363 , ASP A:365 , GLU A:366 , ASP A:434 , ASN A:484 , TRP A:486 , HOH A:1116 , HOH A:1249 , HOH A:1377binding site for residue TRS A 1001
2AC2SOFTWARETYR A:100 , PHE A:450 , GLY A:533 , MET A:534 , ILE A:567 , HOH A:1202binding site for residue EDO A 1002
3AC3SOFTWARETYR A:515 , ALA A:519 , ARG A:522 , ASP A:575 , ASP A:576 , HOH A:1122binding site for residue EDO A 1003
4AC4SOFTWAREHIS A:122 , TYR A:373 , ARG A:418 , ASP A:434 , HOH A:1258binding site for residue EDO A 1004
5AC5SOFTWAREPHE A:601 , ARG A:653 , TYR A:655 , HOH A:1277 , HOH A:1432binding site for residue EDO A 1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:206 -Pro A:207
2Tyr A:274 -Pro A:275
3Gly A:369 -Tyr A:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XPO)

(-) 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:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeee.....hhhhhhh...hhhhhhh.............eeeee..eeeeeee......eee............eeeeeee.........ee.....eeee...eeeeee....eeeee..............................eeeeee...eeeeeee...hhhhhhhhhhhhh......hhhhh.eeee.....hhhhhhhhhhhhhhhh....eeeehhhhh................hhhhhhhhhhhh..eeeeee.........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh..eeee.....................hhhhhhhhhhhhhhhhhhhhhhhh.....eee...........eee.....hhhhhhhhhhhhh....ee........hhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............eee...eee.........eeee....eeee.....eeee..eeee........eeee...eeee.............eeeeeee.....eeeeeee.....hhhhhh..eeeeeeeee.....eeeee..........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpo A  29 NWTEIYPGVWKATVGKPESYDLLKAAGAQPNKDALSKTEKVSFPFANGGVSLEVSGGKTYLRFPLQKEEQLYGFGLNFQTVHQRGKILELHVDHYGGKDSGRTHAPTPFYVSSNGYGVFINSARYIKVWAGTGVRKDSENFPTPKDRNTDKTWSSRPYSDAVEILVPAEGVEVYVFGGPKPIDAVKRYNLLNGGGYLPPRWGLGFTQRVMTRYTDKDVEKEVNDFKEKGYPLDFVGLEPGWQSKAYPGTFSWDKSRYPDPTSFVKKMKDQGIRLNLWINPYISPDAPFYKEIKPYTGSHTVWLGLVPDFTMAEARKPFFNQLLKDQIERGVSGYKIDEVDGYDYYLWPDAAKFPSGLSAEQMRQTYGLLVQRYSAELYKQRNERTFGLVRASNGGGTSFPYVIYNDYYNHQDFITALINSGFAGVLWTPEVRASKSGEEWLRRFQSNVFSPMAMINAWASGTKPWSYPEVEADVKKFALLRMQMMPYWYSAFARYHFEGMPPFRGMGLESKEIKDQYMAGDDLLVAPMFAGEKSRKVVLPKGKWYDFYTGEYAGDGEVLDVTPGLDKIPVYVRDGGIVPMMPALLNSPKSNQKVDLEIRYYGNKPGEFKLYDDDGETFNYEKGDFSWRTIRVEKDKSGKVKGSISAAVKGKVNTVGKVTFTAMTK 719
                                    38        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       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      537|                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       564
   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 4XPO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4XPO)

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  Cis Peptide Bonds
    Gly A:206 - Pro A:207   [ RasMol ]  
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    Tyr A:274 - Pro A:275   [ RasMol ]  
 
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  4xpo
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  A0A0F7R6D6_9 | A0A0F7R6D6
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  3.2.1.22
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0F7R6D6_9 | A0A0F7R6D6: 4xpp 4xpq 4xpr 4xps

(-) Related Entries Specified in the PDB File

4xpp THE SAME PROTEIN COMPLEXED WITH D-GALACTOSE
4xpq THE SAME PROTEIN COMPLEXED WITH L-FUCOSE
4xpr THE MUTANT D365A
4xps THE MUTANT D365A COMPLEXED WITH P-NITROPHENYL-ALPHA-D- GALACTOPYRANOSIDE