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(-) Description

Title :  UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
 
Authors :  A. K. Singh, B. Pluvinage, M. A. Higgins, A. B. Dalia, M. Flynn, A. R. Lloy J. N. Weiser, K. A. Stubbs, A. B. Boraston, S. J. King
Date :  17 Mar 14  (Deposition) - 20 Aug 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Singh, B. Pluvinage, M. A. Higgins, A. B. Dalia, S. A. Woodiga, M. Flynn, A. R. Lloyd, J. N. Weiser, K. A. Stubbs, A. B. Boraston, S. J. King
Unravelling The Multiple Functions Of The Architecturally Intricate Streptococcus Pneumoniae Beta-Galactosidase, Bgaa
Plos Pathog. V. 10 04364 2014
PubMed-ID: 25210925  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004364

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE
    Chains: A, B
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 1463-1645
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: NCH18

 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  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:1495 , ASP B:1498 , LEU B:1500 , ASN B:1509 , THR B:1636 , GLU B:1637BINDING SITE FOR RESIDUE CA B2644
02AC2SOFTWAREASN A:1495 , ASP A:1498 , LEU A:1500 , ASN A:1509 , THR A:1636 , GLU A:1637BINDING SITE FOR RESIDUE CA A2644
03AC3SOFTWAREASP A:1491 , ARG A:1510 , THR A:1512 , ASP A:1548 , HOH A:2172 , HOH A:2363BINDING SITE FOR RESIDUE EDO A2645
04AC4SOFTWAREASP B:1491 , ARG B:1510 , THR B:1512 , ASP B:1548 , HOH B:2329BINDING SITE FOR RESIDUE EDO B2645
05AC5SOFTWAREPHE A:1483 , SER A:1485 , SER A:1522 , VAL A:1577 , GLY A:1578 , PHE A:1584 , ASN A:1585 , ARG A:1621BINDING SITE FOR RESIDUE EDO A2646
06AC6SOFTWARESER A:1490 , ASP A:1491 , PRO A:1492 , ASN A:1495 , ALA A:1508 , ASN A:1509 , ARG A:1510 , HOH A:2364BINDING SITE FOR RESIDUE EDO A2647
07AC7SOFTWAREGLN A:1473 , SER A:1477 , GLU A:1478 , PRO A:1480 , HOH A:2110 , HOH A:2119 , HOH A:2121 , HOH A:2365 , HOH A:2366BINDING SITE FOR RESIDUE EDO A2648
08AC8SOFTWARETHR A:1566 , VAL A:1567 , THR A:1569 , HIS A:1582 , VAL A:1583 , HOH A:2287 , HOH A:2367BINDING SITE FOR RESIDUE EDO A2649
09AC9SOFTWARESER B:1490 , ASP B:1491 , PRO B:1492 , ASN B:1495 , ALA B:1508 , ASN B:1509 , ARG B:1510BINDING SITE FOR RESIDUE EDO B2646
10BC1SOFTWARESER B:1485 , GLU B:1520 , ALA B:1521 , SER B:1522 , ARG B:1621 , ARG B:1623 , HOH B:2170 , HOH B:2309BINDING SITE FOR RESIDUE EDO B2647
11BC2SOFTWAREMSE A:1607 , HIS A:1609 , HOH A:2329 , ASN B:1573 , ASN B:1579BINDING SITE FOR RESIDUE EDO B2648
12BC3SOFTWAREARG A:1536 , SER A:1537 , HOH A:2209 , HOH A:2368BINDING SITE FOR RESIDUE EDO A2650
13BC4SOFTWARESER B:1556 , TYR B:1557 , HOH B:2331BINDING SITE FOR RESIDUE EDO B2649

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:1479 -Pro A:1480
2Gln A:1506 -Pro A:1507
3Leu B:1479 -Pro B:1480
4Gln B:1506 -Pro B:1507

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CUA)

(-) 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:178
 aligned with Q8DQP4_STRR6 | Q8DQP4 from UniProtKB/TrEMBL  Length:2228

    Alignment length:178
                                  1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605      1615      1625      1635        
        Q8DQP4_STRR6   1466 QGANISDQWTGSELPLAFASDSNPSDPVSNVNDKLISYNNQPANRWTNWNRSNPEASVGVLFGDSGILSKRSVDNLSVGFHEDHGVGAPKSYVIEYYVGKTVPTAPKNPSFVGNEDHVFNDSANWKPVTNLKAPAQLKAGEMNHFSFDKVETYAIRIRMVKADNKRGTSITEVQIFAK 1643
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee.......hhhhhhh............ee.......eeeeeee.ee..ee..eeeeeeeeee..........eeeeeee..........hhhhhhhh.hhhhhhh.eee..............eeeeeeeeeee.eeeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4cua A 1466 QGANISDQWTGSELPLAFASDSNPSDPVSNVNDKLISYNNQPANRWTNWNRSNPEASVGVLFGDSGILSKRSVDNLSVGFHEDHGVGAPKSYVIEYYVGKTVPTAPKNPSFVGNEDHVFNDSANWKPVTNLKAPAQLKAGEmNHFSFDKVETYAIRIRmVKADNKRGTSITEVQIFAK 1643
                                  1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605 |    1615      1625      1635        
                                                                                                                                                                      1607-MSE         1624-MSE               


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with Q8DQP4_STRR6 | Q8DQP4 from UniProtKB/TrEMBL  Length:2228

    Alignment length:178
                                  1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605      1615      1625      1635        
        Q8DQP4_STRR6   1466 QGANISDQWTGSELPLAFASDSNPSDPVSNVNDKLISYNNQPANRWTNWNRSNPEASVGVLFGDSGILSKRSVDNLSVGFHEDHGVGAPKSYVIEYYVGKTVPTAPKNPSFVGNEDHVFNDSANWKPVTNLKAPAQLKAGEMNHFSFDKVETYAIRIRMVKADNKRGTSITEVQIFAK 1643
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...........eeee.......hhhhhhh............ee.......eeeeeee.ee..ee..eeeeeeeeee.....ee.eeeeeeeee..........hhhhhhhh.hhhhhhh.eee..............eeeeeeeeeee.eeeeeeee.....eeeeeeee.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4cua B 1466 QGANISDQWTGSELPLAFASDSNPSDPVSNVNDKLISYNNQPANRWTNWNRSNPEASVGVLFGDSGILSKRSVDNLSVGFHEDHGVGAPKSYVIEYYVGKTVPTAPKNPSFVGNEDHVFNDSANWKPVTNLKAPAQLKAGEmNHFSFDKVETYAIRIRmVKADNKRGTSITEVQIFAK 1643
                                  1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605 |    1615      1625      1635        
                                                                                                                                                                      1607-MSE         1624-MSE
   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 4CUA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8DQP4_STRR6 | Q8DQP4)
molecular function
    GO:0004565    beta-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  4cua
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 Related Entries

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

UniProtKB/TrEMBL
        Q8DQP4_STRR6 | Q8DQP4: 4cu9 4cub

(-) Related Entries Specified in the PDB File

4cu6 UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
4cu7 UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
4cu8 UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
4cu9 UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
4cub UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA
4cuc UNRAVELLING THE MULTIPLE FUNCTIONS OF THE ARCHITECTURALLY INTRICATE STREPTOCOCCUS PNEUMONIAE BETA-GALACTOSIDASE, BGAA.