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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 :  02 Jun 11  (Deposition) - 21 Sep 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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
    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  (4, 72)

Asymmetric/Biological Unit (4, 72)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3IOD67Ligand/IonIODIDE ION
4PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

(-) Sites  (60, 60)

Asymmetric Unit (60, 60)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:361 , HOH A:2026 , HOH A:2299 , HOH A:2300 , HOH A:2301 , HOH A:2302 , HOH A:2484BINDING SITE FOR RESIDUE CA A1615
02AC2SOFTWAREASP A:477 , ASP A:485 , HOH A:2228 , HOH A:2448 , HOH A:2449 , HOH A:2594BINDING SITE FOR RESIDUE CA A1616
03AC3SOFTWARETYR A:317 , LYS A:370 , SER A:373 , GLU A:384 , TYR A:386 , GLY A:445 , HOH A:2354BINDING SITE FOR RESIDUE PE4 A1617
04AC4SOFTWAREARG A:196 , TYR A:482 , TRP A:517 , ASP A:519 , HOH A:2026 , HOH A:2302BINDING SITE FOR RESIDUE EDO A1618
05AC5SOFTWAREASP A:360 , GLU A:361 , PHE A:415 , TRP A:439 , TYR A:469 , TRP A:517 , HOH A:2213 , HOH A:2300BINDING SITE FOR RESIDUE EDO A1619
06AC6SOFTWAREGLU A:543 , HOH A:2012BINDING SITE FOR RESIDUE IOD A1620
07AC7SOFTWARELYS A:210BINDING SITE FOR RESIDUE IOD A1621
08AC8SOFTWAREGLU A:503BINDING SITE FOR RESIDUE IOD A1622
09AC9SOFTWAREPRO A:521 , SER A:522BINDING SITE FOR RESIDUE IOD A1623
10BC1SOFTWARELYS A:452 , GLU A:456BINDING SITE FOR RESIDUE IOD A1624
11BC2SOFTWAREHOH A:2165BINDING SITE FOR RESIDUE IOD A1625
12BC3SOFTWAREASN A:609BINDING SITE FOR RESIDUE IOD A1627
13BC4SOFTWAREASP A:400 , HOH A:2368BINDING SITE FOR RESIDUE IOD A1628
14BC5SOFTWARELYS A:306 , ASN A:312 , ASN A:489 , ASN A:493 , IOD A:1656 , HOH A:2460BINDING SITE FOR RESIDUE IOD A1629
15BC6SOFTWARETHR A:497 , SER A:498BINDING SITE FOR RESIDUE IOD A1630
16BC7SOFTWARETHR A:595BINDING SITE FOR RESIDUE IOD A1631
17BC8SOFTWAREHOH A:2365BINDING SITE FOR RESIDUE IOD A1632
18BC9SOFTWAREARG A:524 , HOH A:2445BINDING SITE FOR RESIDUE IOD A1633
19CC1SOFTWARELYS A:205BINDING SITE FOR RESIDUE IOD A1634
20CC2SOFTWARELYS A:501BINDING SITE FOR RESIDUE IOD A1636
21CC3SOFTWAREARG A:524 , ARG A:529BINDING SITE FOR RESIDUE IOD A1637
22CC4SOFTWAREASN A:539 , ARG A:590BINDING SITE FOR RESIDUE IOD A1639
23CC5SOFTWAREARG A:524 , SER A:526 , SER A:528BINDING SITE FOR RESIDUE IOD A1640
24CC6SOFTWAREPRO A:508 , ILE A:509 , LYS A:579 , IOD A:1642 , HOH A:2019 , HOH A:2338BINDING SITE FOR RESIDUE IOD A1641
25CC7SOFTWARELYS A:186 , IOD A:1641 , HOH A:2019BINDING SITE FOR RESIDUE IOD A1642
26CC8SOFTWAREGLN A:311 , HOH A:2230 , HOH A:2450BINDING SITE FOR RESIDUE IOD A1643
27CC9SOFTWAREASN A:399BINDING SITE FOR RESIDUE IOD A1645
28DC1SOFTWAREGLN A:332BINDING SITE FOR RESIDUE IOD A1646
29DC2SOFTWAREGLU A:202 , HOH A:2096BINDING SITE FOR RESIDUE IOD A1647
30DC3SOFTWAREARG A:324 , ASN A:364 , HOH A:2299BINDING SITE FOR RESIDUE IOD A1648
31DC4SOFTWAREGLY A:445 , ASP A:447 , HOH A:2148 , HOH A:2416BINDING SITE FOR RESIDUE IOD A1649
32DC5SOFTWARESER A:583 , HOH A:2086BINDING SITE FOR RESIDUE IOD A1650
33DC6SOFTWAREGLU A:353 , HOH A:2294 , IOD A:9010BINDING SITE FOR RESIDUE IOD A1651
34DC7SOFTWAREGLU A:254 , HOH A:2160BINDING SITE FOR RESIDUE IOD A1652
35DC8SOFTWAREASN A:258BINDING SITE FOR RESIDUE IOD A1653
36DC9SOFTWAREGLU A:569 , HOH A:2262BINDING SITE FOR RESIDUE IOD A1654
37EC1SOFTWAREGLN A:460 , GLU A:576BINDING SITE FOR RESIDUE IOD A1655
38EC2SOFTWAREASN A:312 , ASN A:314 , LYS A:321 , IOD A:1629 , HOH A:2232 , HOH A:2466BINDING SITE FOR RESIDUE IOD A1656
39EC3SOFTWAREGLN A:203 , PRO A:527 , IOD A:1662 , HOH A:2298 , HOH A:2488BINDING SITE FOR RESIDUE IOD A1657
40EC4SOFTWARETHR A:567BINDING SITE FOR RESIDUE IOD A1658
41EC5SOFTWAREGLU A:206 , IOD A:1662BINDING SITE FOR RESIDUE IOD A1659
42EC6SOFTWAREALA A:568 , HOH A:2403BINDING SITE FOR RESIDUE IOD A1660
43EC7SOFTWAREARG A:251BINDING SITE FOR RESIDUE IOD A1661
44EC8SOFTWAREGLU A:206 , IOD A:1657 , IOD A:1659 , HOH A:2038BINDING SITE FOR RESIDUE IOD A1662
45EC9SOFTWAREASN A:422 , SER A:423 , VAL A:448BINDING SITE FOR RESIDUE IOD A1665
46FC1SOFTWAREHOH A:2540BINDING SITE FOR RESIDUE IOD A1666
47FC2SOFTWAREASP A:594 , HOH A:2572 , IOD A:9009BINDING SITE FOR RESIDUE IOD A1667
48FC3SOFTWARELYS A:197 , ASN A:265 , TYR A:525BINDING SITE FOR RESIDUE IOD A1668
49FC4SOFTWARELYS A:411 , LYS A:575 , HOH A:2546 , IOD A:9011BINDING SITE FOR RESIDUE IOD A1669
50FC5SOFTWAREMET A:180 , ASN A:181 , HOH A:2002 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE IOD A1670
51FC6SOFTWAREASN A:539 , IOD A:9005BINDING SITE FOR RESIDUE IOD A1671
52FC7SOFTWAREGLY A:241 , ARG A:565BINDING SITE FOR RESIDUE IOD A1672
53FC8SOFTWARELEU A:612BINDING SITE FOR RESIDUE IOD A9001
54FC9SOFTWAREIOD A:1671 , HOH A:2280 , HOH A:2495BINDING SITE FOR RESIDUE IOD A9005
55GC1SOFTWAREHOH A:2179 , HOH A:2217 , HOH A:2281BINDING SITE FOR RESIDUE IOD A9006
56GC2SOFTWAREHOH A:2082BINDING SITE FOR RESIDUE IOD A9007
57GC3SOFTWAREIOD A:1667 , HOH A:2352BINDING SITE FOR RESIDUE IOD A9009
58GC4SOFTWAREIOD A:1651 , IOD A:9011BINDING SITE FOR RESIDUE IOD A9010
59GC5SOFTWAREIOD A:1669 , HOH A:2546 , IOD A:9010BINDING SITE FOR RESIDUE IOD A9011
60GC6SOFTWARELYS A:406 , ASP A:562 , HOH A:2373 , HOH A:2534BINDING SITE FOR RESIDUE IOD A9013

(-) SS Bonds  (0, 0)

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

(-) 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 2YLL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YLL)

(-) 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:436
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:436
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608      
           STRH_STRPN   179 TVNEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLTP 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...........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
                 2yll A 179 AMNEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLTP 614
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608
   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 2YLL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  STRH_STRPN | P49610
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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 4az5 4az6 4az7 4azb 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