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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSYNTHASE MUTANT E727A OF ESCHERICHIA COLI GH63 GLYCOSIDASE IN COMPLEX WITH GLUCOSE AND LACTOSE
 
Authors :  T. Miyazaki, T. Tonozuka
Date :  08 Sep 16  (Deposition) - 12 Oct 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Gh63 Alpha, Alpha Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Miyazaki, A. Nishikawa, T. Tonozuka
Crystal Structure Of The Enzyme-Product Complex Reveals Sugar Ring Distortion During Catalysis By Family 63 Inverting Alpha-Glycosidase
J. Struct. Biol. V. 196 479 2016
PubMed-ID: 27688023  |  Reference-DOI: 10.1016/J.JSB.2016.09.015

(-) Compounds

Molecule 1 - GLUCOSIDASE YGJK
    Chains: A, B
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: YGJK
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CA2Ligand/IonCALCIUM ION
3LBT2Ligand/IonALPHA-LACTOSE
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3LBT1Ligand/IonALPHA-LACTOSE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3LBT1Ligand/IonALPHA-LACTOSE
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:431 , ASN A:433 , ASN A:435 , VAL A:437 , GLU A:439 , GLU A:549binding site for residue CA A 1001
2AC2SOFTWAREASP A:274 , HOH A:1235 , HOH A:1313binding site for residue MG A 1002
3AC3SOFTWAREPRO A:308 , PHE A:315 , TRP A:321 , TRP A:323 , ASP A:324 , LYS A:391 , GLY A:499 , ASP A:501 , TRP A:680 , PHE A:742 , TRP A:744 , LBT A:1004binding site for residue BGC A 1003
4AC4SOFTWARETRP A:321 , ASP A:368 , LEU A:369 , ASN A:386 , LYS A:391 , TRP A:496 , ASP A:501 , BGC A:1003 , HOH A:1136 , HOH A:1140 , HOH A:1203 , LYS B:464binding site for residue LBT A 1004
5AC5SOFTWAREASP B:431 , ASN B:433 , ASN B:435 , VAL B:437 , GLU B:439 , GLU B:549binding site for residue CA B 1001
6AC6SOFTWAREASP B:538 , THR B:540 , HOH B:1332 , HOH B:1345 , HOH B:1359 , HOH B:1362binding site for residue MG B 1002
7AC7SOFTWAREPRO B:308 , PHE B:315 , TRP B:321 , TRP B:323 , ASP B:324 , LYS B:391 , GLY B:499 , ASP B:501 , TYR B:679 , TRP B:680 , TRP B:685 , PHE B:742 , TRP B:744 , LBT B:1004 , HOH B:1141binding site for residue BGC B 1003
8AC8SOFTWAREASP A:463 , LYS A:464 , TRP B:314 , TRP B:321 , ASP B:368 , ASN B:384 , ASN B:386 , LYS B:391 , TRP B:496 , ASP B:501 , TYR B:679 , BGC B:1003 , HOH B:1105 , HOH B:1124 , HOH B:1374binding site for residue LBT B 1004

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:594 -A:617
2B:594 -B:617

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GW7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GW7)

(-) Exons   (0, 0)

(no "Exon" information available for 5GW7)

(-) 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:758
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........eeeee.................ee................ee......ee.eeeeeeeeeee..ee...eeeeeee..eeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeeee..eeeee..ee....hhhhhh.....eeeee..eeeee....ee...ee.....eeeeee....eeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhee.........ee..............hhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhh...........hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee............eeeeee..eeeeeehhhhhhhhhhhh...eeehhhhhhhhhhhh...hhhhh..hhhhhhhhhhh..hhhhh...eeeee.....eeeeee.eehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhee....ee..ee..............hhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh.............................eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........ee......ee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gw7 A   1 NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQANYNPLTGAQQGAPNFSWSAAHLYMLYNDFFR 758
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Chain B from PDB  Type:PROTEIN  Length:760
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........eee...................ee...............eee......eeeeeeeeeeeeee..ee...eeeeeee..eeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeeee..eee..........hhhhhh.....eeeee..eeeee....ee...ee.....eeeeee....eeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhee.........ee..............hhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhh...........hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee............eeeeee..eeeeeehhhhhhhhhhh....eeehhhhhhhhhhh....hhhhh..hhhhhhhhhhh..hhhhhh..eeee........eeee.eehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhee....ee..ee..............hhhhh.hhhhhhhhhh...hhhhhhhhhhhhh..............................eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........eeee......eeeee.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gw7 B   1 NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQANYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQ 760
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   Legend:   → Mismatch (orange background)
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  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 5GW7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GW7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GW7)

(-) Gene Ontology  (10, 10)

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  5gw7
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  YGJK_ECOLI | P42592
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  3.2.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        YGJK_ECOLI | P42592: 3d3i 3w7s 3w7t 3w7u 3w7w 3w7x 5ca3

(-) Related Entries Specified in the PDB File

3d3i UNLIGANDED FORM OF THE SAME PROTEIN
3w7s THE SAME PROTEIN COMPLEXED WITH GLUCOSE
3w7t THE SAME PROTEIN COMPLEXED WITH MANNOSE
3w7u THE SAME PROTEIN COMPLEXED WITH GALACTOSE
3w7w THE MUTANT E727A COMPLEXED WITH 2-O-ALPHA-D-GLUCOPYRANOSYL-ALPHA-D- GALACTOPYRANOSE
3w7x THE MUTANT D324N COMPLEXED WITH MELIBIOSE
5ca3 THE MUTANT D324N COMPLEXED WITH GLUCOSE AND LACTOSE