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(-) Description

Title :  PRODUCT COMPLEX OF A MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA
 
Authors :  A. Lammerts Van Bueren, E. Ficko-Blean, B. Pluvinage, J. H. Hehemann M. A. Higgins, L. Deng, A. D. Ogunniyi, U. H. Stroeher, N. E. Warry, R. D. M. Czjzek, J. C. Paton, D. J. Vocadlo, A. B. Boraston
Date :  17 Feb 11  (Deposition) - 20 Apr 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lammerts Van Bueren, E. Ficko-Blean, B. Pluvinage, J. Hehemann, M. A. Higgins, L. Deng, A. D. Ogunniyi, U. H. Stroeher, N. El Warry, R. D. Burke, M. Czjzek, J. C. Paton, D. J. Vocadlo, A. B. Boraston
The Conformation And Function Of A Multimodular Glycogen-Degrading Pneumococcal Virulence Factor.
Structure V. 19 640 2011
PubMed-ID: 21565699  |  Reference-DOI: 10.1016/J.STR.2011.03.001

(-) Compounds

Molecule 1 - PUTATIVE ALKALINE AMYLOPULLULANASE
    Atcc: BAA-334D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 135-1143
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: PULLULANASE SPUA GH13

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLC10Ligand/IonALPHA-D-GLUCOSE
3NA5Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:481 , GLY A:512 , ILE A:513 , THR A:514 , ASP A:515 , TYR A:519 , HOH A:3264 , HOH A:3265 , HOH A:3266BINDING SITE FOR RESIDUE SO4 A 2152
2AC2SOFTWARETHR A:898 , LEU A:899 , HIS A:941 , GLN A:944 , HOH A:3515BINDING SITE FOR RESIDUE NA A 2153
3AC3SOFTWAREARG A:652BINDING SITE FOR RESIDUE NA A 2155
4AC4SOFTWARELYS A:583 , ARG A:1035 , HOH A:3325BINDING SITE FOR RESIDUE NA A 2156
5AC5SOFTWAREASP A:353 , HOH A:3083 , HOH A:3175BINDING SITE FOR RESIDUE NA A 2157
6AC6SOFTWARETRP A:156 , TRP A:158 , TRP A:168 , ASN A:210 , ASP A:214 , TYR A:667 , ASP A:668 , ASN A:714 , HIS A:715 , PHE A:743 , ASP A:778 , LYS A:969 , ASP A:989 , TYR A:991 , GLC A:2151 , HOH A:3414 , HOH A:3694 , HOH A:3695 , HOH A:3696 , HOH A:3697 , HOH A:3698 , HOH A:3699 , HOH A:3700 , HOH A:3705BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 2144 TO 2147
7AC7SOFTWARETRP A:809 , ASP A:839 , ARG A:842 , TYR A:849 , ASN A:896 , LYS A:969 , ASP A:989 , GLC A:2145 , GLC A:2146 , HOH A:3470 , HOH A:3475 , HOH A:3583 , HOH A:3694 , HOH A:3703 , HOH A:3704 , HOH A:3705 , HOH A:3706BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 2148 TO 2151
8AC8SOFTWARETRP A:263 , TRP A:265 , TRP A:276 , LEU A:306 , LYS A:318 , ASN A:323 , HOH A:3099 , HOH A:3134 , HOH A:3708 , HOH A:3710BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 2158 TO 2160

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YA1)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Trp A:168 -Pro A:169
2Glu A:194 -Gln A:195
3Trp A:276 -Pro A:277
4Gln A:360 -His A:361
5Tyr A:849 -Pro A:850

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YA1)

(-) Exons   (0, 0)

(no "Exon" information available for 2YA1)

(-) 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:981
 aligned with A0A0H2UNG0_S | A0A0H2UNG0 from UniProtKB/TrEMBL  Length:1280

    Alignment length:1066
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      
        A0A0H2UNG0_S     78 SDISSPGNANASLEKTEEKPAASPADPAPQTGQDRSSEPTTSTSPVTTETKAEEPIEDNYFRIHVKKLPEENKDAQGLWTWDDVEKPSENWPNGALSFKDAKKDDYGYYLDVKLKGEQAKKISFLINNTAGKNLTGDKSVEKLVPKMNEAWLDQDYKVFSYEPQPAGTVRVNYYRTDGNYDKKSLWYWGDVKNPSSAQWPDGTDFTATGKYGRYIDIPLNEAAREFGFLLLDESKQGDDVKIRKENYKFTDLKNHSQIFLKDDDESIYTNPYYVHDIRMTGAQHVGTSSIESSFSTLVGAKKEDILKHSNITNHLGNKVTITDVAIDEAGKKVTYSGDFSDTKHPYTVSYNSDQFTTKTSWRLKDETYSYDGKLGADLKEEGKQVDLTLWSPSADKVSVVVYDKNDPDKVVGTVALEKGERGTWKQTLDSTNKLGITDFTGYYYQYQIERQGKTVLALDPYAKSLAAWNSDDSKIDDAHKVAKAAFVDPAKLGPQDLTYGKIHNFKTREDAVIYEAHVRDFTSDPAIAKDLTKPFGTFEAFIEKLDYLKDLGVTHIQLLPVLSYYFVNELKNHERLSDYASSNSNYNWGYDPQNYFSLTGMYSSDPKNPEKRIAEFKNLINEIHKRGMGAILDVVYNHTAKVDLFEDLEPNYYHFMDADGTPRTSFGGGRLGTTHHMTKRLLIDSIKYLVDTYKVDGFRFDMMGDHDAASIEEAYKAARALNPNLIMLGEGWRTYAGDENMPTKAADQDWMKHTDTVAVFSDDIRNNLKSGYPNEGQPAFITGGKRDVNTIFKNLIAQPTNFEADSPGDVIQYIAAHDNLTLFDIIAQSIKKDPSKAENYAEIHRRLRLGNLMVLTAQGTPFIHSGQEYGRTKQFRDPAYKTPVAEDKVPNKSHLLRDKDGNPFDYPYFIHDSYDSSDAVNKFDWTKATDGKAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVHLITVPGQNGVEKEDVVIGYQITAPNGDIYAVFVNADEKAREFNLGTAFAHLRNAEVLADENQAGPVGIANPKGLEWTEKGLKLNALTATVLRVSQN 1143
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh----------------------------------------------------..eeeeee......hhh.eeeeeee.............ee.hhhee....eeeeee..-....eeeeeeee.........eeee.......eeee.....ee........eeeeeee........eeeeeee.............ee..eee..eeeeeee.......eeeeeee...hhhhh......eee.......eeeee.................eeee..------.eee...-------....eeee.------------......ee.-------.....eeee..eeee...hhhhhhhhhh.....eeeeehhhheeeeeee.....eeeeeee.......eeeeee.ee....eeeeee..............eeeeeeee..eeeee............hhhh..hhhhh...ee..hhhhh..............hhhhh.eeeehhhhhhhhhhhh........hhhhhhhhhhhhhhhh..eeee..........hhhh.....................................hhhhhhhhhhhhhhhh...eeeeee.......hhhhhh................ee..ee.....hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.................hhhhhhhh...eeehhhhhhhhh................eehhhhhhhhh.........hhh.eee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhh...........eeeee.....eeeeeeee......hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhheee...........ee.eeeeeee.....eeeeeee.....eeee....hhhhhhheeee...............eee...eeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ya1 A  130 AHMAS----------------------------------------------------DNYFRIHVKKLPEENKDAQGLWTWDDVEKPSENWPNGALSFKDAKKDDYGYYLDVKLK-EQAKKISFLINNTAGKNLTGDKSVEKLVPKMNEAWLDQDYKVFSYEPQPAGTVRVNYYRTDGNYDKKSLWYWGDVKNPSSAQWPDGTDFTATGKYGRYIDIPLNEAAREFGFLLLDESKQGDDVKIRKENYKFTDLKNHSQIFLKDDDESIYTNPYYVHDIRMTGAQH------ESSFSTL-------ILKHSNITN------------IDEAGKKVT-------TKHPYTVSYNSDQFTTKTSWRLKDETYSYDGKLGADLKEEGKQVDLTLWSPSADKVSVVVYDKNDPDKVVGTVALEKGERGTWKQTLDSTNKLGITDFTGYYYQYQIERQGKTVLALDPYAKSLAAWNSDDSKIDDAHKVAKAAFVDPAKLGPQDLTYGKIHNFKTREDAVIYEAHVRDFTSDPAIAKDLTKPFGTFEAFIEKLDYLKDLGVTHIQLLPVLSYYFVNELKNHERLSDYASSNSNYNWGYDPQNYFSLTGMYSSDPKNPEKRIAEFKNLINEIHKRGMGAILDVVYNHTAKVDLFEDLEPNYYHFMDADGTPRTSFGGGRLGTTHHMTKRLLIDSIKYLVDTYKVDGFRFDMMGDHDAASIEEAYKAARALNPNLIMLGEGWRTYAGDENMPTKAADQDWMKHTDTVAVFSDDIRNNLKSGYPNEGQPAFITGGKRDVNTIFKNLIAQPTNFEADSPGDVIQYIAAHDNLTLFDIIAQSIKKDPSKAENYAEIHRRLRLGNLMVLTAQGTPFIHSGQEYGRTKQFRNPAYRTPVAEDKVPNKSHLLRDKDGNPFDYPYFIHDSYDSSDAVNKFDWTKATDGKAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVHLITVPGQNGVEKEDVVIGYQITAPNGDIYAVFVNADEKAREFNLGTAFAHLRNAEVLADENQAGPVGIANPKGLEWTEKGLKLNALTATVLRVSQN 1143
                                |    -         -         -         -         -       137       147       157       167       177       187    | |197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357   |     -|     |  -    |  387  |      -     | 407   |     - |     427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      
                              134                                                  135                                                      192 |                                                                                                                                                                    361    368   374     382     390          403     411     419                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                              194
   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 2YA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YA1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2YA1)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UNG0_S | A0A0H2UNG0: 2j44 2ya0 2ya2

(-) Related Entries Specified in the PDB File

2j44 ALPHA-GLUCAN BINDING BY A STREPTOCOCCAL VIRULENCE FACTOR
2ya0 CATALYTIC MODULE OF THE MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA
2ya2 CATALYTIC MODULE OF THE MULTI-MODULAR GLYCOGEN-DEGRADING PNEUMOCOCCAL VIRULENCE FACTOR SPUA IN COMPLEX WITH AN INHIBITOR.