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(-) Description

Title :  DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH
 
Authors :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Date :  25 Jun 12  (Deposition) - 10 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Family 20 Glycoside Hydrolase Catalytic Modules In The Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh.
Org. Biomol. Chem. V. 11 7907 2013
PubMed-ID: 24132305  |  Reference-DOI: 10.1039/C3OB41579A

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC MODULE, RESIDUES 181-614
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: GLYCOSIDE HYDROLASE 20

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2OAN2Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
3SO48Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:196 , HIS A:297 , ASP A:360 , GLU A:361 , TRP A:439 , TRP A:443 , ASP A:466 , TYR A:469 , TRP A:517 , ASP A:519 , EDO A:1608 , HOH A:2038 , HOH A:2165 , HOH A:2244 , HOH A:2274 , HOH A:2296BINDING SITE FOR RESIDUE OAN A1606
02AC2SOFTWAREASN A:422BINDING SITE FOR RESIDUE EDO A1607
03AC3SOFTWARETRP A:443 , GLU A:503 , OAN A:1606 , HOH A:2224BINDING SITE FOR RESIDUE EDO A1608
04AC4SOFTWARETYR A:317 , TYR A:386 , HOH A:2127 , HOH A:2297 , HOH A:2298BINDING SITE FOR RESIDUE EDO A1609
05AC5SOFTWARETYR A:317BINDING SITE FOR RESIDUE EDO A1610
06AC6SOFTWARELYS A:452 , GLU A:456 , GLU A:503 , HOH A:2230BINDING SITE FOR RESIDUE EDO A1611
07AC7SOFTWAREGLY A:441 , PRO A:500 , LYS A:501 , THR A:502 , HOH A:2226 , HOH A:2228 , HOH A:2243BINDING SITE FOR RESIDUE SO4 A1612
08AC8SOFTWAREARG A:524 , SER A:526 , PRO A:527 , SER A:528BINDING SITE FOR RESIDUE SO4 A1613
09AC9SOFTWARELYS A:532 , ARG A:535 , HIS A:536BINDING SITE FOR RESIDUE SO4 A1614
10BC1SOFTWAREHIS A:213 , TYR A:214 , ARG A:535BINDING SITE FOR RESIDUE SO4 A1615

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:294 -Pro A:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AZB)

(-) 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:408
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:425
                                   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     
           STRH_STRPN   181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQE 605
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....ee.....eee..eeehhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh.....eeee..eeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh..........eeee...........hhhhhhhhh..eee.hhhhhee...........hhhhhhhhhhhh................eeeeeee........hhhhhhhhhhhhhhhh.......hhhhhhhhhh....-----------------............hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4azb A 181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGGGNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKD-----------------AIRSLDSNLSRAQQDTIDQAIAKLQE 605
                                   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 |       -       580       590       600     
                                                                                                                                                                                                                                                                                                                                                                                                                       562               580
   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 4AZB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (STRH_STRPN | P49610)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        STRH_STRPN | P49610: 2ltj 2yl5 2yl6 2yl8 2yl9 2yla 2yll 4az5 4az6 4az7 4azc 4azg 4azh 4azi

(-) Related Entries Specified in the PDB File

2yl5 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl6 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl8 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl9 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yla INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yll INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
4az5 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az6 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az7 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azc DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azg DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azh DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azi DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH