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(-) Description

Title :  2 BETA-GLUCANS (6-O-GLUCOSYL-LAMINARITRIOSE) IN BOTH DONOR AND ACCEPTOR SITES OF GH16 LAMINARINASE 16A FROM PHANEROCHAETE CHRYSOSPORIUM.
 
Authors :  J. Vasur, R. Kawai, E. Andersson, K. Igarashi, M. Sandgren, M. Samejima, J. Stahlberg
Date :  03 Dec 08  (Deposition) - 21 Jul 09  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A
Keywords :  Laminarin, Family 16, Extracellular, Beta Sandwich, Basidiomycete, Beta- Glucanase, Glycosyl Hydrolase, 3/1, Gh7, Gh16, Lam16A, Beta-1, 6-Glucan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vasur, R. Kawai, E. Andersson, K. Igarashi, M. Sandgren, M. Samejima, J. Stahlberg
X-Ray Crystal Structures Of Phanerochaete Chrysosporium Laminarinase 16A In Complex With Products From Lichenin And Laminarin Hydrolysis
Febs J. V. 276 3858 2009
PubMed-ID: 19769746  |  Reference-DOI: 10.1111/J.1742-4658.2009.07099.X

(-) Compounds

Molecule 1 - PUTATIVE LAMINARINASE
    Chains: A
    EC Number: 3.2.1.6
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: KM71H
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 21-318
    Organism Common: WHITE-ROT FUNGUS
    Organism Scientific: PHANEROCHAETE CHRYSOSPORIUM
    Organism Taxid: 5306
    Strain: K-3
    Synonym: LAMINARINASE 16A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1BGC7Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:43 , ARG A:55 , NAG A:302 , HOH A:2401BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARETYR A:46 , NAG A:301 , BMA A:303 , MAN A:304 , MAN A:307BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWARENAG A:302 , MAN A:304BINDING SITE FOR RESIDUE BMA A 303
04AC4SOFTWARENAG A:302 , BMA A:303 , MAN A:305 , MAN A:307 , HOH A:2105 , HOH A:2402BINDING SITE FOR RESIDUE MAN A 304
05AC5SOFTWAREMAN A:304 , MAN A:306 , HOH A:2390 , HOH A:2403 , HOH A:2404 , HOH A:2405 , HOH A:2406BINDING SITE FOR RESIDUE MAN A 305
06AC6SOFTWAREASN A:220 , ASN A:223 , MAN A:305 , HOH A:2408 , HOH A:2409 , HOH A:2411BINDING SITE FOR RESIDUE MAN A 306
07AC7SOFTWARESER A:48 , GLY A:49 , ASP A:50 , THR A:51 , NAG A:302 , MAN A:304BINDING SITE FOR RESIDUE MAN A 307
08AC8SOFTWARELEU A:62 , SER A:63 , GLY A:161 , BGC A:402 , BGC A:407 , HOH A:2136 , HOH A:2414 , HOH A:2415 , HOH A:2422BINDING SITE FOR RESIDUE BGC A 401
09AC9SOFTWARESER A:63 , GLY A:161 , ASP A:256 , GLN A:260 , BGC A:401 , BGC A:403 , BGC A:404 , HOH A:2416 , HOH A:2417 , HOH A:2418BINDING SITE FOR RESIDUE BGC A 402
10BC1SOFTWAREHIS A:133 , ASN A:162 , ASP A:256 , BGC A:402 , BGC A:404 , BGC A:405 , BGC A:406 , HOH A:2204 , HOH A:2206 , HOH A:2416BINDING SITE FOR RESIDUE BGC A 403
11BC2SOFTWAREASN A:152 , TRP A:257 , GLN A:260 , BGC A:402 , BGC A:403 , HOH A:2258 , HOH A:2260 , HOH A:2359 , HOH A:2419BINDING SITE FOR RESIDUE BGC A 404
12BC3SOFTWAREARG A:73 , TRP A:103 , TRP A:110 , GLU A:115 , BGC A:403 , BGC A:406 , HOH A:2151 , HOH A:2201 , HOH A:2420 , HOH A:2421BINDING SITE FOR RESIDUE BGC A 405
13BC4SOFTWAREPRO A:26 , HIS A:28 , ASP A:256 , BGC A:403 , BGC A:405 , BGC A:407 , HOH A:2416BINDING SITE FOR RESIDUE BGC A 406
14BC5SOFTWARETHR A:59 , THR A:60 , THR A:61 , BGC A:401 , BGC A:406 , HOH A:2422BINDING SITE FOR RESIDUE BGC A 407
15CATAUTHORGLU A:115 , GLU A:120CATALYTIC RESIDUES GLU 115 AS NUCLEOPHILE AND GLU 120 AS ACID-BASE
16NGLAUTHORASN A:43N-GLYCOSYLATION SITE COVALENTLY LINKED TO NAG A 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:96 -A:269
2A:138 -A:236
3A:155 -A:165
4A:254 -A:273

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:110 -Pro A:111
2Ser A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W52)

(-) Exons   (0, 0)

(no "Exon" information available for 2W52)

(-) 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:298
 aligned with Q874E3_PHACH | Q874E3 from UniProtKB/TrEMBL  Length:318

    Alignment length:298
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
         Q874E3_PHACH    21 ATYHLEDNWVGSAFLSTFTHEAIADPTHGRVNYVDQATALAKNLTYASGDTLILRADHTTTLSPSGPGRNSVRIRSIKTYTTHVAVFDVRHMPQGCGTWPAAWETDEGDWPNGGEVDIIEGVNDQSPNAMTLHTGANCAMPASRTMTGHATNNNCDVNTDGNTGCGVQAPTANSYGPSFNANGGGWYAMERTNSFIKVWFFPRNAGNVPNDIASGPATINTDNWGTPTAFFPNTNCDIGSHFDANNIIINLTFCGDWAGQASIFNGAGCPGSCVDYVNNNPSAFANAYWDIASVRVYQ 318
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------Glyco_hydro_16-2w52A01 A:32-163                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhheeee.......eeeeee.hhhhhh..eeeee..eeeeeee.........eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeehhh...eeeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeeee..hhh.eeeeee..hhh.hhhhhh.eeeeeeeeee.eeeeeeeeee......hhhhh..eeeehhh...eeeeeee.ee.hhhheeeeeeeeeeeeehhhh..hhhhhh......hhhhhhh.hhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w52 A   1 ATYHLEDNWVGSAFLSTFTHEAIADPTHGRVNYVDQATALAKNLTYASGDTLILRADHTTTLSPSGPGRNSVRIRSIKTYTTHVAVFDVRHMPQGCGTWPAAWETDEGDWPNGGEVDIIEGVNDQSPNAMTLHTGANCAMPASRTMTGHATNNNCDVNTDGNTGCGVQAPTANSYGPSFNANGGGWYAMERTNSFIKVWFFPRNAGNVPNDIASGPATINTDNWGTPTAFFPNTNCDIGSHFDANNIIINLTFCGDWAGQASIFNGAGCPGSCVDYVNNNPSAFANAYWDIASVRVYQ 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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 2W52)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W52)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q874E3_PHACH | Q874E3)
molecular function
    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.

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  2w52
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  Q874E3_PHACH | Q874E3
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  3.2.1.6
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 Related Entries

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

UniProtKB/TrEMBL
        Q874E3_PHACH | Q874E3: 2cl2 2w39 2wlq 2wne

(-) Related Entries Specified in the PDB File

2cl2 ENDO-1,3(4)-BETA-GLUCANASE FROM PHANEROCHAETE CHRYSOSPORIUM, SOLVED USING NATIVE SULFUR SAD, EXHIBITING INTACT HEPTASACCHARIDE GLYCOSYLATION
2w39 GLC(BETA-1-3)GLC DISACCHARIDE IN -1 AND -2 SITES OF LAMINARINASE 16A FROM PHANEROCHAETE CHRYSOSPORIUM