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(-) Description

Title :  ALPHA-GLUCAN RECOGNITION BY FAMILY 41 CARBOHYDRATE-BINDING MODULES FROM STREPTOCOCCAL VIRULENCE FACTORS
 
Authors :  A. Lammerts Van Bueren, M. Higgins, D. Wang, R. D. Burke, A. B. Boraston
Date :  24 Aug 06  (Deposition) - 11 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Family 41, Pullulanase, Streptococcal, Carbohydrate-Binding Module, Glycogen Binding, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Lammerts Van Bueren, M. Higgins, D. Wang, R. D. Burke, A. B. Boraston
Identification And Structural Basis Of Binding To Host Lung Glycogen By Streptococcal Virulence Factors.
Nat. Struct. Mol. Biol. V. 14 76 2007
PubMed-ID: 17187076  |  Reference-DOI: 10.1038/NSMB1187

(-) Compounds

Molecule 1 - SPYDX
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCARBOHYDRATE-BINDING, RESIDUE 92-310
    Organism ScientificSTREPTOCOCCUS PYOGENES
    Organism Taxid1314
    Other DetailsTANDEM FAMILY 41 CARBOHYDRATE-BINDING MODULES

 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  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2J43)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J43)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:40 -Pro A:41
2Trp A:147 -Pro A:148
3Trp B:41 -Pro B:42
4Trp B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J43)

(-) Exons   (0, 0)

(no "Exon" information available for 2J43)

(-) 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:219
 aligned with Q8KLP1_STRPY | Q8KLP1 from UniProtKB/TrEMBL  Length:1165

    Alignment length:219
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q8KLP1_STRPY    92 AEHHLRMHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITMTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHIPLLTPKMNEVWIDENYHAHAYRPLKKGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGPYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 310
               SCOP domains d2j43a1 A:5-111 Pullulanase PulA                                                                           d2j43a2 A:112-223 Pullulanase PulA                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhh.eeeeeee...................ee....ee..ee.......eeeeeeee.........eeee.......eeee.....ee........eeeeeee........eeeeeee............ee..eee..eeeeeee.......eeeeeee...hhhhh......eee.......eeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j43 A   5 ASHHLRmHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITmTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKmNEVWIDENYHAHAYRPLKEGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 223
                                  | 14        24        34        44  |     54        64        74        84        94 |     104       114       124       134       144       154       164       174       184       194       204       214         
                                 11-MSE                              47-MSE                                           96-MSE                                                                                                                           

Chain A from PDB  Type:PROTEIN  Length:219
 aligned with Q99XX8_STRP1 | Q99XX8 from UniProtKB/TrEMBL  Length:1165

    Alignment length:219
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
         Q99XX8_STRP1    92 AEHHLRMHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITMTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKMNEVWIDENYHAHAYRPLKKGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 310
               SCOP domains d2j43a1 A:5-111 Pullulanase PulA                                                                           d2j43a2 A:112-223 Pullulanase PulA                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhh.eeeeeee...................ee....ee..ee.......eeeeeeee.........eeee.......eeee.....ee........eeeeeee........eeeeeee............ee..eee..eeeeeee.......eeeeeee...hhhhh......eee.......eeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j43 A   5 ASHHLRmHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITmTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKmNEVWIDENYHAHAYRPLKEGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 223
                                  | 14        24        34        44  |     54        64        74        84        94 |     104       114       124       134       144       154       164       174       184       194       204       214         
                                 11-MSE                              47-MSE                                           96-MSE                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q8KLP1_STRPY | Q8KLP1 from UniProtKB/TrEMBL  Length:1165

    Alignment length:218
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
         Q8KLP1_STRPY    93 EHHLRMHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITMTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHIPLLTPKMNEVWIDENYHAHAYRPLKKGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGPYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 310
               SCOP domains d2j43b1 B:7-112 Pullulanase PulA                                                                          d2j43b2 B:113-224 Pullulanase PulA                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhh.eeeeeee...................ee....ee..ee.......eeeeeeee.........eeee.......eeee.....ee........eeeeeee........eeeeeee............ee..eee..eeeeeee.......eeeeeee...hhhhh......eee.......eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j43 B   7 SHHLRmHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITmTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKmNEVWIDENYHAHAYRPLKEGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 224
                                 |  16        26        36        46 |      56        66        76        86        96|      106       116       126       136       146       156       166       176       186       196       206       216        
                                12-MSE                              48-MSE                                           97-MSE                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q99XX8_STRP1 | Q99XX8 from UniProtKB/TrEMBL  Length:1165

    Alignment length:218
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
         Q99XX8_STRP1    93 EHHLRMHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITMTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKMNEVWIDENYHAHAYRPLKKGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 310
               SCOP domains d2j43b1 B:7-112 Pullulanase PulA                                                                          d2j43b2 B:113-224 Pullulanase PulA                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhh.eeeeeee...................ee....ee..ee.......eeeeeeee.........eeee.......eeee.....ee........eeeeeee........eeeeeee............ee..eee..eeeeeee.......eeeeeee...hhhhh......eee.......eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j43 B   7 SHHLRmHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITmTKAKKDDYGYYLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKmNEVWIDENYHAHAYRPLKEGYLRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFLILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYID 224
                                 |  16        26        36        46 |      56        66        76        86        96|      106       116       126       136       146       156       166       176       186       196       206       216        
                                12-MSE                              48-MSE                                           97-MSE                                                                                                                           

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J43)

(-) Gene Ontology  (11, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8KLP1_STRPY | Q8KLP1)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0051060    pullulanase activity    Catalysis of the hydrolysis of (1,6)-alpha-D-glucosidic linkages in pullulan (a linear polymer of alpha-(1,6)-linked maltotriose units) and in amylopectin and glycogen, and the a- and b-limit dextrins of amylopectin and glycogen.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B   (Q99XX8_STRP1 | Q99XX8)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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

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