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(-) Description

Title :  CRYSTAL STRUCTURE OF BIFIDOBACTERIUM BIFIDUM BETA-GALACTOSIDASE
 
Authors :  A. S. Godoy, M. T. Murakami, C. M. Camilo, A. Bernardes, I. Polikarpov
Date :  08 Sep 14  (Deposition) - 30 Sep 15  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Lactase, Family 42 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Godoy, C. M. Camilo, M. A. Kadowaki, H. D. S. Muniz, M. E. Santo, M. T. Murakami, A. S. Nascimento, I. Polikarpov
Crystal Structure Of Beta1-6-Galactosidase From Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants Of The Enzymatic Activity And Its Inhibition By Alpah-Galactose.
Febs J. V. 283 4097 2016
PubMed-ID: 27685756  |  Reference-DOI: 10.1111/FEBS.13908

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE
    Chains: A, B, C
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTA
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: BIFIDOBACTERIUM BIFIDUM S17
    Organism Taxid: 883062
    Other Details: COURTESY OF PROF. CHRISTIAN RIEDEL, ULM UNIVERSITY, GERMANY
    Synonym: BETA-GAL

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4POL5Ligand/IonN-PROPANOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:134 , TYR A:135 , ASN A:138 , HOH A:2971BINDING SITE FOR RESIDUE PEG A 701
02AC2SOFTWAREARG A:122 , ASN A:160 , GLU A:161 , ASP A:287 , GLU A:320 , GLU A:368 , HOH A:2081 , HOH A:2316 , HOH A:2589 , HOH A:2632BINDING SITE FOR RESIDUE GOL A 702
03AC3SOFTWAREHOH A:2317 , HOH A:2319 , HOH A:2380 , HOH A:2385 , HOH A:2972 , HOH A:2973 , HOH A:2974BINDING SITE FOR RESIDUE GOL A 703
04AC4SOFTWAREASP A:69 , HOH A:2975BINDING SITE FOR RESIDUE PEG A 704
05AC5SOFTWAREASP A:74 , HIS A:146 , TYR A:147 , LYS A:148 , ASN A:150 , POL A:706 , HOH A:2210 , HOH A:2364 , HOH A:2976BINDING SITE FOR RESIDUE P6G A 705
06AC6SOFTWAREASP A:74 , ASP A:78 , ASN A:150 , TYR A:152 , P6G A:705BINDING SITE FOR RESIDUE POL A 706
07AC7SOFTWAREARG A:521 , GLY A:525 , VAL A:526 , SER A:562 , THR A:563 , ALA A:564 , HOH A:2812 , HOH A:2814BINDING SITE FOR RESIDUE POL A 707
08AC8SOFTWAREALA A:670 , HIS A:671 , THR A:678 , ASP A:680 , HOH A:2959BINDING SITE FOR RESIDUE POL A 710
09AC9SOFTWAREGLU A:112 , ARG A:113 , GLY A:114 , TYR A:170 , ARG A:215 , TRP C:118BINDING SITE FOR RESIDUE GOL A 711
10BC1SOFTWAREARG B:122 , CYS B:164 , HIS B:165 , TRP B:328 , GOL B:704 , HOH B:2331 , HOH B:2618 , HOH B:2622 , HOH B:2931BINDING SITE FOR RESIDUE GOL B 701
11BC2SOFTWAREARG B:122 , ASN B:160 , GLU B:161 , ASP B:287 , GLU B:320 , PHE B:358 , GLU B:368 , GOL B:704 , HOH B:2091 , HOH B:2330 , HOH B:2622BINDING SITE FOR RESIDUE GOL B 702
12BC3SOFTWAREASP B:74 , HIS B:146 , TYR B:147 , LYS B:148 , ASN B:150 , HOH B:2236BINDING SITE FOR RESIDUE POL B 703
13BC4SOFTWAREARG B:122 , GLU B:161 , MET B:264 , TRP B:328 , GOL B:701 , GOL B:702 , HOH B:2575BINDING SITE FOR RESIDUE GOL B 704
14BC5SOFTWAREARG B:606 , ARG B:651 , THR B:652 , HOH B:2903BINDING SITE FOR RESIDUE GOL B 710
15BC6SOFTWAREHOH A:2481 , ARG C:122 , ASN C:160 , GLU C:161 , ASP C:287 , GLU C:320 , PHE C:358 , GLU C:368 , GOL C:702 , HOH C:2060 , HOH C:2496BINDING SITE FOR RESIDUE GOL C 701
16BC7SOFTWAREARG C:122 , GLU C:161 , CYS C:164 , GOL C:701 , HOH C:2237 , HOH C:2449BINDING SITE FOR RESIDUE GOL C 702
17BC8SOFTWAREASP C:506 , ILE C:511 , HOH C:2631 , HOH C:2633BINDING SITE FOR RESIDUE POL C 710

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:358 -Gln A:359
2Tyr A:516 -Pro A:517
3Phe B:358 -Gln B:359
4Tyr B:516 -Pro B:517
5Phe C:358 -Gln C:359
6Tyr C:516 -Pro C:517

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UZS)

(-) 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:687
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.......hhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.ee.........hhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhh.eeeeee........................hhhhhhhhhhhhhhhhhhhh.....ee....eeeeehhhhhhhhh...........hhhhhhhhhhhhhh....eeee...hhhhh.eeee......hhhhhhhhhhhhhh..eeeee....................hhhhhheeeeeeee...........eee....eeeeeeeeeeee...eeeeeeee.hhhhh....eeeeeeee..eeeeee.eehhhhhhhhhhhhhhhhh.hhhhh....eeeeeee.hhhh.eeeeeee.....eeee...eeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uzs A   3 KRRKHSWPQPLKGAESRLWYGGDYNPDQWPEEVWDDDIRLMKKAGVNLVSVGIFSWAKIEPEEGKYDFDWLDRAIDKLGKAGIAVDLASATASPPMWLTQAHPEVLWKDERGDTVWPGAREHWRPTSPVFREYALNLCRRMAEHYKGNPYVVAWHVSNEYGCHNRFDYSDDAMRAFQKWCKKRYKTIDAVNEAWGTAFWAQHMNDFSEIIPPRYIGDGNFMNPGKLLDYKRFSSDALKELYIAERDVLESITPGLPLTTNFMVSAGGSMLDYDDWGAEVDFVSNDHYFTPGEAHFDEVAYAASLMDGISRKEPWFQMEHSTSAVNWRPINYRAEPGSVVRDSLAQVAMGADAICYFQWRQSKAGAEKWHSSMVPHAGEDSQIFRDVCELGADLGRLSDEGLMGTKTVKSKVAVVFDYESQWATEYTANPTQQVDHWTEPLDWFRALADNGITADVVPVRSDWDSYEIAVLPCVYLLSEETSRRVREFVANGGKLFVTYYTGLSDENDHIWLGGYPGSIRDVVGVRVEEFAPMGNDMPGALDHLDLDNGTVAHDFADVITSTADTSTVLASYKAERWTGMNEVPAIVANGYGDGRTVYVGCRLGRQGLAKSLPAMLGSMGLSDLAGDGRVLRVERADAAAASHFEFVFNRTHEPVTVDVEGEAIAASLAHVDDGRATIDPTGVVVLRR 689
                                    12        22        32        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       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       


Chain B from PDB  Type:PROTEIN  Length:679
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.......hhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.ee.........hhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhh.eeeeee........................hhhhhhhhhhhhhhhhhhhh.....ee....eeeeehhhhhhhhh...........hhhhhhhhhhhhhh....eeee...hhhhh.eeee......hhhhhhhhhhhhhh..eeeee....................hhhhhheeeeeeee...........eee....eeeeeeeeeeee...eeeeeeee.hhhhh....eeeeeeee..eeeeee.eehhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeee...eeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uzs B   4 RRKHSWPQPLKGAESRLWYGGDYNPDQWPEEVWDDDIRLMKKAGVNLVSVGIFSWAKIEPEEGKYDFDWLDRAIDKLGKAGIAVDLASATASPPMWLTQAHPEVLWKDERGDTVWPGAREHWRPTSPVFREYALNLCRRMAEHYKGNPYVVAWHVSNEYGCHNRFDYSDDAMRAFQKWCKKRYKTIDAVNEAWGTAFWAQHMNDFSEIIPPRYIGDGNFMNPGKLLDYKRFSSDALKELYIAERDVLESITPGLPLTTNFMVSAGGSMLDYDDWGAEVDFVSNDHYFTPGEAHFDEVAYAASLMDGISRKEPWFQMEHSTSAVNWRPINYRAEPGSVVRDSLAQVAMGADAICYFQWRQSKAGAEKWHSSMVPHAGEDSQIFRDVCELGADLGRLSDEGLMGTKTVKSKVAVVFDYESQWATEYTANPTQQVDHWTEPLDWFRALADNGITADVVPVRSDWDSYEIAVLPCVYLLSEETSRRVREFVANGGKLFVTYYTGLSDENDHIWLGGYPGSIRDVVGVRVEEFAPMGNDMPGALDHLDLDNGTVAHDFADVITSTADTSTVLASYKAERWTGMNEVPAIVANGYGDGRTVYVGCRLGRQGLAKSLPAMLGSMGLSGDGRVLRVERADSHFEFVFNRTHEPVTVDVEGEAIAASLAHVDDGRATIDPTGVVVLRR 689
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623|      636 ||    650       660       670       680         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     623|        638|                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      627         643                                              


Chain C from PDB  Type:PROTEIN  Length:683
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.......hhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.ee.........hhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhh.eeeeee........................hhhhhhhhhhhhhhhhhhhh.....ee....eeeeehhhhhhhhh...........hhhhhhhhhhhhhh....eeee...hhhhh.eeee......hhhhhhhhhhhhhh..eeeee....................hhhhhheeeeee.............eee....eeeeeeeeeeee....eeeeeee.hhhhh....eeeeeeee..eeeeee.eehhhhhhhhhhhhhhhhh..........eeeeeee..eeeeeee.....eeee...eeeeeeeeeee..eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uzs C   3 KRRKHSWPQPLKGAESRLWYGGDYNPDQWPEEVWDDDIRLMKKAGVNLVSVGIFSWAKIEPEEGKYDFDWLDRAIDKLGKAGIAVDLASATASPPMWLTQAHPEVLWKDERGDTVWPGAREHWRPTSPVFREYALNLCRRMAEHYKGNPYVVAWHVSNEYGCHNRFDYSDDAMRAFQKWCKKRYKTIDAVNEAWGTAFWAQHMNDFSEIIPPRYIGDGNFMNPGKLLDYKRFSSDALKELYIAERDVLESITPGLPLTTNFMVSAGGSMLDYDDWGAEVDFVSNDHYFTPGEAHFDEVAYAASLMDGISRKEPWFQMEHSTSAVNWRPINYRAEPGSVVRDSLAQVAMGADAICYFQWRQSKAGAEKWHSSMVPHAGEDSQIFRDVCELGADLGRLSDEGLMGTKTVKSKVAVVFDYESQWATEYTANPTQQVDHWTEPLDWFRALADNGITADVVPVRSDWDSYEIAVLPCVYLLSEETSRRVREFVANGGKLFVTYYTGLSDENDHIWLGGYPGSIRDVVGVRVEEFAPMGNDMPGALDHLDLDNGTVAHDFADVITSTADTSTVLASYKAERWTGMNEVPAIVANGYGDGRTVYVGCRLGRQGLAKSLPAMLGSMGLSDLAGDGRVLRVERADSHFEFVFNRTHEPVTVDVEGEAIAASLAHVDDGRATIDPTGVVVLRR 689
                                    12        22        32        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       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632     ||646       656       666       676       686   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     638|                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      643
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4UZS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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        E3EPA1_BIFBS | E3EPA1: 4ucf

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