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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSYNTHASE MUTANT D324N OF ESCHERICHIA COLI GH63 GLYCOSIDASE IN COMPLEX WITH GLUCOSE AND LACTOSE
 
Authors :  T. Miyazaki, T. Tonozuka
Date :  29 Jun 15  (Deposition) - 10 Aug 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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. 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 Plasmid: PYGJK-SIG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YGJK, B3080, JW3051
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12

 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  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA2Ligand/IonCALCIUM ION
3GLC1Ligand/IonALPHA-D-GLUCOSE
4LBT2Ligand/IonALPHA-LACTOSE
5MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BGC-1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GLC-1Ligand/IonALPHA-D-GLUCOSE
4LBT1Ligand/IonALPHA-LACTOSE
5MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GLC1Ligand/IonALPHA-D-GLUCOSE
4LBT1Ligand/IonALPHA-LACTOSE
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
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:1218 , HOH A:1553binding site for residue MG A 1002
3AC3SOFTWAREHOH A:1270 , HOH A:1277 , HOH A:1341 , HOH A:1599 , HOH A:1676 , HOH B:1189binding site for residue MG A 1003
4AC4SOFTWARETRP A:314 , TRP A:321 , ASP A:368 , ASN A:386 , LYS A:391 , ASP A:501 , HOH A:1125 , HOH A:1153 , HOH A:1235 , HOH A:1451 , ASP B:463 , 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:1458 , HOH B:1477 , HOH B:1527 , HOH B:1562binding site for residue MG B 1002
7AC7SOFTWAREPRO B:308 , PHE B:315 , TRP B:321 , TRP B:323 , ASN B:324 , LYS B:391 , GLY B:499 , ASP B:501 , TYR B:679 , TRP B:680 , TRP B:685 , GLU B:727 , PHE B:742 , TRP B:744 , LBT B:1004binding 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 , BGC B:1003 , HOH B:1116 , HOH B:1139 , HOH B:1164 , HOH B:1273 , HOH B:1292 , HOH B:1449binding site for residue LBT B 1004
9AC9SOFTWARETHR B:170 , ASP B:172 , LYS B:175 , GLN B:196 , HIS B:198 , GLN B:241 , HOH B:1159 , HOH B:1242 , HOH B:1286binding site for residue GLC B 1005

(-) 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 5CA3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CA3)

(-) Exons   (0, 0)

(no "Exon" information available for 5CA3)

(-) 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................eee....eee.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..........ee.............eeeeee..eeeeeehhhhhhhhhhhh...eeehhhhhhhhhhhh...hhhhh..hhhhhhhhhhh..hhhhh...eeeee.....eeeeee.eehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhee....ee..ee..............hhhhh.hhhhhhhhhh...hhhhhhhhhhhhh..............................eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........ee......ee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ca3 A   1 NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWNTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFR 758
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Chain B from PDB  Type:PROTEIN  Length:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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....eeehhhhhhhhhhhh...hhhhh..hhhhhhhhhhh..hhhhhh..eeee........eeee.eehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhee....ee..ee..............hhhhh.hhhhhhhhhh...hhhhhhhhhhhhh...............................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........eeee......eeeee.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ca3 B   1 NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWNTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRK 759
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750
   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 5CA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CA3)

(-) Gene Ontology  (10, 10)

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  5ca3
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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 5gw7

(-) 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
5ca4