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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LAMINARINASE CATALYTIC DOMAIN FROM THERMOTOGA MARITIMA MSB8
 
Authors :  W. Y. Jeng, N. C. Wang, A. H. J. Wang
Date :  03 Jun 11  (Deposition) - 23 Nov 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta-Jelly Roll Fold, Glycosyl Hydrolase Family 16, Laminarinase, Endo-1, 3-Beta-Glucanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Y. Jeng, N. C. Wang, C. T. Lin, L. F. Shyur, A. H. Wang
Crystal Structures Of The Laminarinase Catalytic Domain Fro Thermotoga Maritima Msb8 In Complex With Inhibitors: Essential Residues For Beta-1, 3 And Beta-1, 4 Glucan Selection.
J. Biol. Chem. V. 286 45030 2011
PubMed-ID: 22065588  |  Reference-DOI: 10.1074/JBC.M111.271213

(-) Compounds

Molecule 1 - LAMINARINASE
    Chains: A, B, C, D
    EC Number: 3.2.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL-21 (DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 204-466
    Gene: TM_0024
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8, ATCC43589

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:17 , ASP A:19 , GLY A:61 , ASP A:249 , HOH A:420 , HOH A:462BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREARG A:252 , HOH A:736 , HOH A:769BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREASN A:45 , TRP A:116 , GLU A:132 , GLU A:137 , HOH A:1117 , HOH A:1155BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREGLU B:17 , ASP B:19 , GLY B:61 , ASP B:249 , HOH B:438 , HOH B:773BINDING SITE FOR RESIDUE CA B 301
05AC5SOFTWAREGLY B:33 , ASN B:34 , GLY B:35 , HIS B:36 , ALA B:37 , TYR B:50 , ASP B:74 , TYR B:76 , TYR B:79BINDING SITE FOR RESIDUE SO4 B 304
06AC6SOFTWAREARG B:252 , HOH B:608 , HOH B:1113BINDING SITE FOR RESIDUE SO4 B 302
07AC7SOFTWAREASN B:45 , ALA B:114 , TRP B:116 , GLU B:132 , ASP B:134 , GLU B:137 , HOH B:517BINDING SITE FOR RESIDUE SO4 B 303
08AC8SOFTWAREGLU C:17 , ASP C:19 , GLY C:61 , ASP C:249 , HOH C:530 , HOH C:614BINDING SITE FOR RESIDUE CA C 301
09AC9SOFTWAREGLY C:33 , ASN C:34 , GLY C:35 , HIS C:36 , ALA C:37 , TYR C:50 , ASP C:74 , TYR C:76 , TYR C:79 , HOH C:818BINDING SITE FOR RESIDUE SO4 C 304
10BC1SOFTWARETYR C:250 , ARG C:252 , HOH C:417 , HOH C:802BINDING SITE FOR RESIDUE SO4 C 302
11BC2SOFTWAREASN C:45 , ALA C:114 , TRP C:116 , GLU C:132 , GLU C:137BINDING SITE FOR RESIDUE SO4 C 303
12BC3SOFTWAREGLY C:170 , HOH C:1153BINDING SITE FOR RESIDUE SO4 C 305
13BC4SOFTWAREALA A:208 , HOH D:1154BINDING SITE FOR RESIDUE SO4 D 305
14BC5SOFTWAREGLU D:17 , ASP D:19 , GLY D:61 , ASP D:249 , HOH D:381 , HOH D:597BINDING SITE FOR RESIDUE CA D 301
15BC6SOFTWARETYR D:250 , ARG D:252 , HOH D:910BINDING SITE FOR RESIDUE SO4 D 302
16BC7SOFTWAREASN D:45 , ALA D:114 , TRP D:116 , GLU D:132 , GLU D:137 , HOH D:1157BINDING SITE FOR RESIDUE SO4 D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AZY)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Trp A:127 -Pro A:128
2Phe A:242 -Pro A:243
3Trp B:127 -Pro B:128
4Phe B:242 -Pro B:243
5Trp C:127 -Pro C:128
6Phe C:242 -Pro C:243
7Trp D:127 -Pro D:128
8Phe D:242 -Pro D:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AZY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AZY)

(-) Exons   (0, 0)

(no "Exon" information available for 3AZY)

(-) 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:251
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:251
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459 
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh....ee....eeee..eeeeeeeeeeee....eeeeee.eee.....ee..eeeeeeee......eeeeeeeee.hhhhhh.....eeeeee.......eeeeeee...........eeee............eeeeeeee..eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azy A   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 258
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:251
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459 
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh...eee....eeee..eeeeeeeeeeeee..eeeeeee.eee.....ee..eeeeeeee......eeeeeeeee.hhhhhh.....eeeeeee......eeeeeee....hhhhheeeeee............eeeeeee...eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azy B   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 258
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 


Chain C from PDB  Type:PROTEIN  Length:251
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:251
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459 
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh...eee....eeee..eeeeeeeeeeee....eeeeee.eee.....ee..eeeeeeee......eeeeeeeee.hhhhhh.....eeeeeee......eeeeeee.........eeeeee............eeeeeeee..eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azy C   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 258
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257 


Chain D from PDB  Type:PROTEIN  Length:251
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:251
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459 
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh...eee....eeee..eeeeeeeeeeee....eeeeee.eee.....ee..eeeeeeee......eeeeeeeee.hhhhhh.....eeeeeee......eeeeeee....hhhhheeeeee............eeeeeee...eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azy D   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMN 258
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   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 3AZY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AZY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AZY)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9WXN1_THEMA | Q9WXN1)
molecular function
    GO:0042973    glucan endo-1,3-beta-D-glucosidase activity    Catalysis of the hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9WXN1_THEMA | Q9WXN1: 1gui 3azx 3azz 3b00 3b01

(-) Related Entries Specified in the PDB File

3azx 3azz 3b00 3b01