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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC MODULE OF A FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71 IN COMPLEX WITH THE A-TRISACCHARIDE BLOOD GROUP ANTIGEN.
 
Authors :  M. A. Higgins, G. E. Whitworth, N. El Warry, M. Randriantsoa, E. Samain, R. D. Burke, D. J. Vocadlo, A. B. Boraston
Date :  30 Jun 09  (Deposition) - 14 Jul 09  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Hydrolase, Fucose Utilization, Blood Group Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Higgins, G. E. Whitworth, N. El Warry, M. Randriantsoa, E. Samain, R. D. Burke, D. J. Vocadlo, A. B. Boraston
Differential Recognition And Hydrolysis Of Host Carbohydrate-Antigens By Streptococcus Pneumoniae Family 98 Glycoside Hydrolases.
J. Biol. Chem. V. 284 26161 2009
PubMed-ID: 19608744  |  Reference-DOI: 10.1074/JBC.M109.024067

(-) Compounds

Molecule 1 - FUCOLECTIN-RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Fragment: CATALYTIC MODULE, RESIDUES 422-1005
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: SP3-BS71
    Synonym: GLYCOSIDE HYDROLASE
 
Molecule 2 - FUCOLECTIN-RELATED PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Fragment: CATALYTIC MODULE, RESIDUES 422-1005
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: SP3-BS71
    Synonym: GLYCOSIDE HYDROLASE

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:481 , TRP A:659 , GLU A:710 , HIS A:711 , PRO A:712 , LYS A:929 , GAL A:2007 , FUC A:2008 , HOH A:3232 , HOH A:3471 , HOH A:3472 , HOH A:3473 , HOH A:3474BINDING SITE FOR RESIDUE A2G A2006
2AC2SOFTWAREGLU A:558 , TRP A:659 , TYR A:662 , GLU A:663 , A2G A:2006 , FUC A:2008 , HOH A:3475 , HOH A:3476 , HOH A:3477BINDING SITE FOR RESIDUE GAL A2007
3AC3SOFTWARETYR A:440 , HIS A:479 , THR A:523 , THR A:557 , GLU A:558 , GLU A:710 , A2G A:2006 , GAL A:2007 , HOH A:3231 , HOH A:3478BINDING SITE FOR RESIDUE FUC A2008
4AC4SOFTWAREASP B:481 , TRP B:659 , GLU B:710 , HIS B:711 , PRO B:712 , LYS B:929 , GAL B:2007 , FUC B:2008 , HOH B:3236 , HOH B:3259 , HOH B:3536 , HOH B:3537 , HOH B:3538 , HOH B:3539BINDING SITE FOR RESIDUE A2G B2006
5AC5SOFTWAREGLU B:558 , TRP B:659 , TYR B:662 , GLU B:663 , A2G B:2006 , FUC B:2008 , HOH B:3540 , HOH B:3541 , HOH B:3542 , HOH B:3543BINDING SITE FOR RESIDUE GAL B2007
6AC6SOFTWARETYR B:440 , HIS B:479 , THR B:523 , THR B:557 , GLU B:558 , GLU B:710 , A2G B:2006 , GAL B:2007 , HOH B:3544 , HOH B:3545 , HOH B:3546BINDING SITE FOR RESIDUE FUC B2008

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:710 -His A:711
2Glu B:710 -His B:711
3Lys B:798 -Thr B:799

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WMI)

(-) 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:572
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhh.........hhhhhhhhh...hhh.eeeeee........hhhhhhhhhhhhhhhh.............eeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh.....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhh..............hhhhhh...hhhhhhhhhhhhhh....eeeeehhhhhhee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeee.hhhhhhhhhhhh.....................ee........eeee..hhhhhhhhhhhhhhhhhh........eeeee..eeeee.........eeeeee....eeeeee....eeeeeee..eeeeeee.....hhhhhh...hhhhhhh....hhhhhhhhhhhhh.........eeeeeeee......eeeeeee........eeeeehhh.eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wmi A  422 VDKRREINNEHPLLMMPLYANGEEFNQGKYTFWGGDTLTGKWENIPDDLKPYTVIQLHPDDLPKRDGAARDFYEHMLEEAAKYVNPKTGKNEPIPVILTVYTAGNMPYYTSAHWLSTSWIDKMYQKYPNLHGIFSTENYWIWANDIENKAADYLKVSAKNGGYFIWAEQNNGSAIEKAFGKNGKIAFQKSVDKYWKNLIFMFKNTPAAEGNDSTTESYMKGLWLSNHTYQWGGLMDTWKWYETGKWKLFASGNIGKSQGDRQWLTEPESMLGEEALGVYLNGGVVYNFEHPAYTYGVNNKESLLFSEVIKEFFRYVIAHPAPSKEKVLEDTKVFIHGDYSNKGNGKFFVNVNTDREQTPLYMTGRYNVIPAIPGVLKTDIQIKEITSPEFSSTQARKEYLNKLYPMNYEGDIFAQKLDNRWFVYNYKVNENVKQTGKLKFNSLEMNVEFEPHTYGIFERISNGLKVNLNNFRTNKDSLWSNAQDANQAKKLPQLTKKGAIKWIEEHYIKDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTITINSNGNLEFELHF 1005
                                   431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003  
                                                                                                                                                                                                                                                                                                                                                                                                                    800|                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                     813                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:571
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhh..........hhhhhhhhh...hhh.eeeeee........hhhhhhhhhhhhhhhhh............eeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhh..............hhhhhh...hhhhhhhhhhhhhh....eeeeehhhhhhee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeee.hhhhhhhhhhh......................ee.......eeee..hhhhhhhhhhhhhhhhhh........eeeee..eeeee.........eeeeeee..eeeeeee....eeeeeee..eeeeeee.....hhhhhh...hhhhhhh....hhhhhhhhhhhhh.........eeeeeeee......eeeeeee........eeeee....eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wmi B  422 VDKRREINNEHPLLMMPLYANGEEFNQGKYTFWGGDTLTGKWENIPDDLKPYTVIQLHPDDLPKRDGAARDFYEHMLEEAAKYVNPKTGKNEPIPVILTVYTAGNMPYYTSAHWLSTSWIDKMYQKYPNLHGIFSTENYWIWANDIENKAADYLKVSAKNGGYFIWAEQNNGSAIEKAFGKNGKIAFQKSVDKYWKNLIFMFKNTPAAEGNDSTTESYMKGLWLSNHTYQWGGLMDTWKWYETGKWKLFASGNIGKSQGDRQWLTEPESMLGEEALGVYLNGGVVYNFEHPAYTYGVNNKESLLFSEVIKEFFRYVIAHPAPSKSKVLEDTKVFIHGDYSNKGNGKFFVNVNTDREQTPLYMTGRYNVIPAIPGVLKTIQIKEITSPEFSSTQARKEYLNKLYPMNYEGDIFAQKLDNRWFVYNYKVNENVKQTGKLKFNSLEMNVEFEPHTYGIFERISNGLKVNLNNFRTNKDSLWSNAQDANQAKKLPQLTKKGAIKWIEEHYIKDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTITINSNGNLEFELHF 1005
                                   431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004 
                                                                                                                                                                                                                                                                                                                                                                                                                   799|                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                    813
   Legend:   → Mismatch (orange background)
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  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 2WMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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    (no "Gene Ontology" information available for 2WMI)

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(-) Related Entries Specified in the PDB File

2wmj CRYSTAL STRUCTURE OF THE CATALYTIC MODULE OF A FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71 (SP3GH98) IN COMPLEX WITH THE B-TRISACCHARIDE BLOOD GROUP ANTIGEN.
2wmk CRYSTAL STRUCTURE OF THE CATALYTIC MODULE OF A FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71 (SP3GH98) IN COMPLEX WITH THE A-LEWISY PENTASACCHARIDE BLOOD GROUP ANTIGEN.