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(-) Description

Title :  INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
 
Authors :  B. Pluvinage, M. A. Higgins, D. W. Abbott, C. Robb, A. B. Dalia, L. Deng, J. N. Weiser, T. B. Parsons, A. J. Fairbanks, D. J. Vocadlo, A. B. Borast
Date :  31 May 11  (Deposition) - 07 Sep 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pluvinage, M. A. Higgins, D. W. Abbott, C. Robb, A. B. Dalia, L. Deng, J. N. Weiser, T. B. Parsons, A. J. Fairbanks, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Pneumococcal Virulence Factor Strh And Molecular Insights Into N-Glycan Recognition And Hydrolysis
Structure V. 19 1603 2011
PubMed-ID: 22078560  |  Reference-DOI: 10.1016/J.STR.2011.08.011

(-) 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: RESIDUES 181-614
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: GLYCOSIDE HYDROLASE GH20

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MAN1Ligand/IonALPHA-D-MANNOSE
4MN9Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:329 , HOH A:2257 , HOH A:2258 , HOH A:2259 , HOH A:2260 , HOH A:2359BINDING SITE FOR RESIDUE MN A1615
02AC2SOFTWAREASP A:477 , ASP A:485 , HOH A:2455 , HOH A:2466BINDING SITE FOR RESIDUE MN A1616
03AC3SOFTWAREASN A:422 , ASP A:447 , HOH A:2393 , HOH A:2394 , HOH A:2640BINDING SITE FOR RESIDUE MN A1617
04AC4SOFTWAREASP A:259 , HOH A:2124 , HOH A:2126 , HOH A:2127 , HOH A:2128 , HOH A:2641BINDING SITE FOR RESIDUE MN A1618
05AC5SOFTWAREASP A:247 , ASN A:608 , HOH A:2089 , HOH A:2642BINDING SITE FOR RESIDUE MN A1619
06AC6SOFTWAREASP A:585BINDING SITE FOR RESIDUE MN A1620
07AC7SOFTWAREGLU A:550 , GLU A:553 , MN A:1622 , MN A:1623 , HOH A:2548BINDING SITE FOR RESIDUE MN A1621
08AC8SOFTWAREGLU A:550 , MN A:1621 , HOH A:2051 , HOH A:2544BINDING SITE FOR RESIDUE MN A1622
09AC9SOFTWAREGLU A:550 , MN A:1621 , HOH A:2548 , HOH A:2645BINDING SITE FOR RESIDUE MN A1623
10BC1SOFTWARETYR A:317 , PHE A:318 , SER A:373 , TYR A:381 , TYR A:386 , HOH A:2236 , HOH A:2335 , HOH A:2646BINDING SITE FOR RESIDUE 15P A1624
11BC2SOFTWAREASN A:422 , ASP A:424BINDING SITE FOR RESIDUE 15P A1625
12BC3SOFTWAREARG A:196 , HIS A:297 , ASP A:360 , GLN A:361 , PHE A:415 , TRP A:439 , TYR A:469 , TYR A:482 , TRP A:517 , ASP A:519 , MAN A:1627 , HOH A:2061 , HOH A:2449BINDING SITE FOR RESIDUE NAG A1626
13BC4SOFTWAREGLN A:361 , ASN A:364 , TRP A:443 , TYR A:482 , ASP A:519 , NAG A:1626 , HOH A:2022 , HOH A:2314 , HOH A:2465 , HOH A:2648BINDING SITE FOR RESIDUE MAN A1627
14BC5SOFTWAREPHE A:315 , ASP A:327 , LEU A:328 , ASP A:329 , TYR A:362 , LEU A:375 , HOH A:2260BINDING SITE FOR RESIDUE EDO A1628

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YL8)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YL8)

(-) Exons   (0, 0)

(no "Exon" information available for 2YL8)

(-) 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:434
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:434
                                   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    
           STRH_STRPN   181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLTP 614
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....ee.....eee..eeehhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh....eeee..eeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhh..........eeee...........hhhhhhhh...eee.hhhhhee...........hhhhhhhhhhhh................eeeeeee........hhhhhhhhhhhhhhhh.......hhhhhhhhhh........hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yl8 A 181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDQYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLTP 614
                                   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
   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 2YL8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YL8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YL8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological 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 2yl9 2yla 2yll 4az5 4az6 4az7 4azb 4azc 4azg 4azh 4azi

(-) Related Entries Specified in the PDB File

2yl5 INHIBITION OF THE PNEUMOCCOCAL 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
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