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(-) Description

Title :  STRUCTURE OF A POLYISOPRENOID BINDING DOMAIN FROM SACCHAROPHAGUS DEGRADANS IMPLICATED IN PLANT CELL WALL BREAKDOWN
 
Authors :  F. Vincent, D. Dal Molin, R. M. Weiner, Y. Bourne, B. Henrissat
Date :  19 Jan 10  (Deposition) - 23 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbohydrate-Binding Protein, Oxidoreduction, Marine Bacteria, Polyisoprenoid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Vincent, D. Dalmolin, R. M. Weiner, Y. Bourne, B. Henrissat
Structure Of A Polyisoprenoid Binding Domain From Saccharophagus Degradans Implicated In Plant Cell Wall Breakdown
Febs Lett. V. 584 1577 2010
PubMed-ID: 20227408  |  Reference-DOI: 10.1016/J.FEBSLET.2010.03.015

(-) Compounds

Molecule 1 - CELLULOSE-BINDING PROTEIN
    Atcc: 43961
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector: PDEST17
    Fragment: YCEI-LIKE DOMAIN, RESIDUES 199-371
    Organism Scientific: SACCHAROPHAGUS DEGRADANS
    Organism Taxid: 203122
    Other Details: OCTAPRENYL PYROPHOSPHATE BOUND TO THE PROTEIN
    Strain: 2-40
    Synonym: X158

 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1IMD3Ligand/IonIMIDAZOLE
2OTP2Ligand/Ion(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2OTP1Ligand/Ion(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2OTP1Ligand/Ion(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:18 , ALA A:41 , ARG A:57 , VAL A:76 , VAL A:78 , VAL A:80 , ILE A:135 , ALA A:153 , LEU A:155 , SER A:159 , VAL A:162 , PHE A:166 , LEU A:168 , TYR A:170 , HOH A:2145BINDING SITE FOR RESIDUE OTP A1174
2AC2SOFTWARELYS B:18 , ALA B:41 , ARG B:57 , ARG B:60 , VAL B:80 , ILE B:135 , ALA B:153 , LEU B:155 , VAL B:162 , PHE B:166 , LEU B:168 , TYR B:170 , HOH B:2239BINDING SITE FOR RESIDUE OTP B1174
3AC3SOFTWAREGLN A:128 , ASN A:129 , GLN A:130 , IMD A:1175 , GLN B:128 , ASN B:129 , GLN B:130 , IMD B:1176BINDING SITE FOR RESIDUE IMD B1175
4AC4SOFTWAREGLN A:128 , ASN A:129 , ASP A:165 , VAL A:167 , IMD B:1175 , IMD B:1176BINDING SITE FOR RESIDUE IMD A1175
5AC5SOFTWAREIMD A:1175 , GLN B:128 , ASN B:129 , ASP B:165 , VAL B:167 , IMD B:1175BINDING SITE FOR RESIDUE IMD B1176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X32)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X32)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X32)

(-) Exons   (0, 0)

(no "Exon" information available for 2X32)

(-) 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:174
 aligned with Q21LI5_SACD2 | Q21LI5 from UniProtKB/TrEMBL  Length:371

    Alignment length:174
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367    
         Q21LI5_SACD2   198 ELAYSLDATASFLNFVSSKKTHVLETHRFDVLSGGISTAGEAQLVIDLNSVNTGIDVRNGRMRDYLFETATYSVATVTVPVDLAAVAGLAVGEDMLVDVSATLDLHGVPGVIDTQLNVQRLSATRIMVQNQSPLLIKAADYSLEAGIETLRNLASLNVISTTVPVDFVLFYEAP 371
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee...eeeeeee..eeeeee...eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeee.....eeeeeeeeeee....eeeeee........hhhhhhhhhhhhhhhh.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x32 A   0 HLAYSLDATASFLNFVSSKKTHVLETHRFDVLSGGISTAGEAQLVIDLNSVNTGIDVRNGRMRDYLFETATYSVATVTVPVDLAAVAGLAVGEDMLVDVSATLDLHGVPGVIDTQLNVQRLSATRIMVQNQSPLLIKAADYSLEAGIETLRNLASLNVISTTVPVDFVLFYEAP 173
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q21LI5_SACD2 | Q21LI5 from UniProtKB/TrEMBL  Length:371

    Alignment length:176
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365      
         Q21LI5_SACD2   196 EPELAYSLDATASFLNFVSSKKTHVLETHRFDVLSGGISTAGEAQLVIDLNSVNTGIDVRNGRMRDYLFETATYSVATVTVPVDLAAVAGLAVGEDMLVDVSATLDLHGVPGVIDTQLNVQRLSATRIMVQNQSPLLIKAADYSLEAGIETLRNLASLNVISTTVPVDFVLFYEAP 371
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Trypan_PARP-2x32------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Trypan_PARP-2x32------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----YceI-2x32B03 B:2-171                                                                                                                                                      -- Pfam domains (3)
           Pfam domains (4) ----YceI-2x32B04 B:2-171                                                                                                                                                      -- Pfam domains (4)
         Sec.struct. author ...eeeee.hhhheeeeeeee...eeeeeee..eeeeee...eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeee....eeeeee........hhhhhhhhhhhhhhhhh......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x32 B  -2 HHHLAYSLDATASFLNFVSSKKTHVLETHRFDVLSGGISTAGEAQLVIDLNSVNTGIDVRNGRMRDYLFETATYSVATVTVPVDLAAVAGLAVGEDMLVDVSATLDLHGVPGVIDTQLNVQRLSATRIMVQNQSPLLIKAADYSLEAGIETLRNLASLNVISTTVPVDFVLFYEAP 173
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167
   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 2X32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X32)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Trypan_PARP] (2)
(-)
Clan: no clan defined [family: YceI] (5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q21LI5_SACD2 | Q21LI5)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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: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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        Q21LI5_SACD2 | Q21LI5: 2x34

(-) Related Entries Specified in the PDB File

2x34 STRUCTURE OF A POLYISOPRENOID BINDING DOMAIN FROM SACCHAROPHAGUS DEGRADANS IMPLICATED IN PLANT CELL WALL BREAKDOWN