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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSTRIDIUM PERFRINGENS BETA-GLUCURONIDASE
 
Authors :  B. D. Wallace, M. R. Redinbo
Date :  09 Mar 13  (Deposition) - 17 Sep 14  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (2x),B (2x),C (1x),D (1x)
Keywords :  Alpha/Beta Barrel, Beta-Sandwich, Sugar-Binding Domain, Glycosyl Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Wallace, A. B. Roberts, R. M. Pollet, J. D. Ingle, K. A. Biernat, S. J. Pellock, M. K. Venkatesh, L. Guthrie, S. K. O'Neal, S. J. Robinson M. Dollinger, E. Figueroa, S. R. Mcshane, R. D. Cohen, J. Jin, S. V. Frye W. C. Zamboni, C. Pepe-Ranney, S. Mani, L. Kelly, M. R. Redinbo
Structure And Inhibition Of Microbiome Beta-Glucuronidases Essential To The Alleviation Of Cancer Drug Toxicity.
Chem. Biol. V. 22 1238 2015
PubMed-ID: 26364932  |  Reference-DOI: 10.1016/J.CHEMBIOL.2015.08.005

(-) Compounds

Molecule 1 - BETA-GLUCURONIDASE
    Chains: A, B
    EC Number: 3.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG9
    Expression System Strain: BL21-AI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BGLR
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 195102
    Strain: 13 / TYPE A
 
Molecule 2 - MALTOSE-BINDING PERIPLASMIC PROTEIN
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG9
    Expression System Strain: BL21-AI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B4034, JW3994, MALE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: MBP, MMBP, MALTODEXTRIN-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A (2x)B (2x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4JKM)

(-) Sites  (0, 0)

(no "Site" information available for 4JKM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Val A:46 -Pro A:47
2Thr A:91 -His A:92
3Leu A:141 -Pro A:142
4Phe A:363 -Met A:364
5Trp A:550 -Asn A:551
6Val B:46 -Pro B:47
7Thr B:91 -His B:92
8Leu B:141 -Pro B:142
9Gly B:233 -Lys B:234
10Trp B:550 -Asn B:551
11Lys D:38 -Asp D:39
12Lys C:314 -Ser C:315

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JKM)

(-) 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:602
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..eeeeeee......hhhhhhh.....eeeee.ee......hhhhhh...eeeeeeee..hhhhh..eeeeee.....eeeeee..eeeeeee.....eeee.........eeeeeeee..........eeeeeeee..eeeeeeee........ee...eeeeee...eeeeeeeeeeee..eeeeeeeeeee...eeeeeee.....eeeeee..eeeeee.............eeeeeeeee..eeeeeeeeee....eeee..eeee..ee..eeeee............hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh.eeeee......................hhhhhh.hhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh.....eeeee.................eeee..........hhhhhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhhhhhh....eeeeeee............................hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jkm A  -2 SNAMLYPIITESRQLIDLSGIWKFKLNEGNGLTEELSKAPLEDTIEMAVPSSYNDLVESQEVRDHVGWVWYERNFTIPKTLLNERIVLRFGSATHEAKVYLNGELLVEHKGGFTPFEAEINDLLVSGDNRLTVAVNNIIDETTLPVGLVKEVEVDGKKVIKNSVNFDFFNYAGIHRPVKIYTTPKSYIEDITIVTDFKENNGYVNYEVQAVGKCNIKVTIIDEENNIVAEGEGKEGKLTINNVHLWEPMNAYLYKLKVELLDDEEIIDTYFEEFGVRTVEVKDGKFLINNKPFYFKGFGKHEDSYVNGRGINEAINIKDFNLMKWIGANSFRTSHYPYSEEIMRLADREGIVVIDETPAVGLHLNFMATGFGGDAPKRDTWKEIGTKEAHERILRELVSRDKNHPCVVMWSVANEPDSDSEGAKEYFEPLIKLTKELDPQKRPVTVVTYLMSTPDRCKVGDIVDVLCLNRYYGWYVAGGDLEEAKRMLEDELKGWEERCPKTPIMFTEYGADTVAGLHDTVPVMFTEEYQVEYYKANHEVMDKCKNFVGEQVWNFADFATSQGIIRVQGNKKGIFTRERKPKMIAHSLRERWTNIPEFGYKK 599
                                     7        17        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       487       497       507       517       527       537       547       557       567       577       587       597  


Chain B from PDB  Type:PROTEIN  Length:602
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..eeeeeee......hhhhhhh.....eeeee.ee......hhhhhh...eeeeeeee..hhhhh..eeeeee.....eeeeee..eeeeeee.....eeee.........eeeeeeee..........eeeeeee....eeeeeee........ee...eeeeee...eeeeeeeeeeee..eeeeeeeeeee...eeeeeee.....eeeeee..eeeeeee............eeeeeeeee..eeeeeeeeee....eeee..eeee..ee..eeeee............hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh.eeeee......................hhhhhh.hhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh.....eeee..................eeee..........hhhhhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhhhhhh....eeeeeee............................hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jkm B  -2 SNAMLYPIITESRQLIDLSGIWKFKLNEGNGLTEELSKAPLEDTIEMAVPSSYNDLVESQEVRDHVGWVWYERNFTIPKTLLNERIVLRFGSATHEAKVYLNGELLVEHKGGFTPFEAEINDLLVSGDNRLTVAVNNIIDETTLPVGLVKEVEVDGKKVIKNSVNFDFFNYAGIHRPVKIYTTPKSYIEDITIVTDFKENNGYVNYEVQAVGKCNIKVTIIDEENNIVAEGEGKEGKLTINNVHLWEPMNAYLYKLKVELLDDEEIIDTYFEEFGVRTVEVKDGKFLINNKPFYFKGFGKHEDSYVNGRGINEAINIKDFNLMKWIGANSFRTSHYPYSEEIMRLADREGIVVIDETPAVGLHLNFMATGFGGDAPKRDTWKEIGTKEAHERILRELVSRDKNHPCVVMWSVANEPDSDSEGAKEYFEPLIKLTKELDPQKRPVTVVTYLMSTPDRCKVGDIVDVLCLNRYYGWYVAGGDLEEAKRMLEDELKGWEERCPKTPIMFTEYGADTVAGLHDTVPVMFTEEYQVEYYKANHEVMDKCKNFVGEQVWNFADFATSQGIIRVQGNKKGIFTRERKPKMIAHSLRERWTNIPEFGYKK 599
                                     7        17        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       487       497       507       517       527       537       547       557       567       577       587       597  


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee.eeeee............hhhhhhhhhhh...eee.....hhhhhhhhhh....eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeeeeehhhhhhhhhh....eeee............eee..................hhhhhhhh...........hhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jkm C 111 KLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSS 378
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    || 306       316       326       336       346       356       366       376  
                                                                                                                                                                                                        285|                                                                            
                                                                                                                                                                                                         302                                                                            


Chain D from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.................hhhhhhhhhh...........eeeeehhhhhhhhhh........hhhhhhhhhhhhhhh.ee..ee.eeeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhh....eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeeeeehhhhhhhhhhh...eeee............eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jkm D  18 IWINGDKAYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSS 379
                                    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
   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 4JKM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:233 - Lys B:234   [ RasMol ]  
    Leu A:141 - Pro A:142   [ RasMol ]  
    Leu B:141 - Pro B:142   [ RasMol ]  
    Lys C:314 - Ser C:315   [ RasMol ]  
    Lys D:38 - Asp D:39   [ RasMol ]  
    Phe A:363 - Met A:364   [ RasMol ]  
    Thr A:91 - His A:92   [ RasMol ]  
    Thr B:91 - His B:92   [ RasMol ]  
    Trp A:550 - Asn A:551   [ RasMol ]  
    Trp B:550 - Asn B:551   [ RasMol ]  
    Val A:46 - Pro A:47   [ RasMol ]  
    Val B:46 - Pro B:47   [ RasMol ]  
 
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  Q8XP19_CLOPE | Q8XP19
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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
        MALE_ECOLI | P0AEX9: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2nvu 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csb 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwf 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5hzw 5i04 5i69 5ihj 5ii5 5iic 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6

(-) Related Entries Specified in the PDB File

4jkk 4jkl