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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, THE FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71, IN COMPLEX WITH THE BLOOD GROUP B ANTIGEN
 
Authors :  M. A. Higgins, E. Ficko-Blean, C. Wright, P. J. Meloncelli, T. L. Lowary A. B. Boraston
Date :  19 Apr 11  (Deposition) - 22 Jun 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Carbohydrate-Binding Module, Blood Group Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Higgins, E. Ficko-Blean, C. Wright, P. J. Meloncelli, T. L. Lowary, A. B. Boraston
The Overall Architecture And Receptor Binding Of Pneumococcal Carbohydrate Antigen Hydrolyzing Enzymes.
J. Mol. Biol. V. 411 1017 2011
PubMed-ID: 21767550  |  Reference-DOI: 10.1016/J.JMB.2011.06.035

(-) Compounds

Molecule 1 - BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: CBM51-1.2, RESIDUES 66-413
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Other Details: TANDEM FAMILY 51 CBMS
    Strain: SP3-BS71

 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  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLA2Ligand/IonALPHA D-GALACTOSE
5NA2Ligand/IonSODIUM ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4GLA1Ligand/IonALPHA D-GALACTOSE
5NA-1Ligand/IonSODIUM ION
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4GLA1Ligand/IonALPHA D-GALACTOSE
5NA-1Ligand/IonSODIUM ION
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:161 , ALA A:211 , HIS A:214 , ASP A:218 , HOH A:2022BINDING SITE FOR RESIDUE CA A1417
2AC2SOFTWAREASP A:343 , GLY A:394 , THR A:397 , ALA A:399 , ASP A:400BINDING SITE FOR RESIDUE NA A1418
3AC3SOFTWAREASP B:343 , SER B:393 , GLY B:394 , THR B:397 , ALA B:399 , ASP B:400BINDING SITE FOR RESIDUE NA B1417
4AC4SOFTWAREVAL B:161 , ALA B:211 , HIS B:214 , ASP B:218BINDING SITE FOR RESIDUE CA B1418
5AC5SOFTWAREASP A:80 , ILE A:81 , ASP A:82 , LYS A:85 , THR A:94 , ASN A:153 , ARG A:156 , HIS A:159 , THR A:215 , TRP A:216 , GLY A:217 , GLU A:219 , SER A:361 , HOH A:2101BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1413 TO 1416
6AC6SOFTWARESER A:75 , VAL A:129 , SER A:131 , ASP B:80 , ILE B:81 , ASP B:82 , LYS B:85 , THR B:94 , ASN B:153 , HIS B:159 , THR B:215 , TRP B:216 , GLY B:217 , GLU B:219 , HOH B:2028BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 1413 TO 1416

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:126 -Pro A:127
2Asn A:308 -Pro A:309
3Ser B:126 -Pro B:127
4Asn B:308 -Pro B:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YGM)

(-) 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:351
 aligned with C1CB04_STRP7 | C1CB04 from UniProtKB/TrEMBL  Length:1005

    Alignment length:351
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411 
         C1CB04_STRP7    62 DKEMTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh...ee...........ee..hhhhhhh.....eeee.....eeee..eee......eeeeee.......eeeeeeee...............eeeeee..eeeee...............eeeeee......eeeeeee.........eeeeeeeeeee......hhhhhhhh...eee.hhh...ee...........ee..hhhhhhh.....eeeee..eeeee..eeeee....eeeeee.....eeeeeeeee..............eeeeeeee..eeeee.hhh...........eeeeee......eeeeeeee.......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ygm A  62 HMASTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411 


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with C1CB04_STRP7 | C1CB04 from UniProtKB/TrEMBL  Length:1005

    Alignment length:394
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408    
         C1CB04_STRP7    19 SFLGSNLVYADVVQSNSNNRASTETARVTGNNLEKLITKDKEIDKEMTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2ygmB01 B:244-411                                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2ygmB02 B:244-411                                                                                                                                                 - Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2ygmB03 B:244-411                                                                                                                                                 - Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NPCBM-2ygmB04 B:244-411                                                                                                                                                 - Pfam domains (4)
         Sec.struct. author .eeee------------------------------------------ee.hhh...ee...........ee..hhhhhhhh....eeee.....eeee..eee......eeeeee.......eeeeeeee...............eeeeee..eeeee...............eeeeee......eeeeeee.........eeeeeeeeeeee.....hhhhhhhh...eee.hhh...ee...........ee..hhhhhhh.....eeeee..eeeee..eeeee....eeeeee.....eeeeeeeee..............eeeeeeee...eeee...............eeeeee......eeeeeeee.......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ygm B  61 SHMAS------------------------------------------TYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDDKVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAVVDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATHGDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSSIKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMAN 412
                                |    -         -         -         -       |68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408    
                               65                                         66
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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 2YGM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: NPCBM] (4)

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

UniProtKB/TrEMBL
        C1CB04_STRP7 | C1CB04: 2ygl

(-) Related Entries Specified in the PDB File

2ygl THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, THE FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71