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(-) Description

Title :  CRYSTAL STRUCTURES OF COMPLEX F. SUCCINOGENES 1,3-1,4-BETA-D-GLUCANASE AND BETA-1,3-1,4-CELLOTRIOSE
 
Authors :  L. C. Tsai, L. F. Shyur, Y. S. Cheng, S. H. Lee
Date :  10 May 05  (Deposition) - 10 May 06  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glucanase/1, 3-1, 4-Beta-D-Glucanase, Beta-1, 3-1, 4-Cellotriose (Cltr), Active Cleft, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Tsai, L. F. Shyur, Y. S. Cheng, S. H. Lee
Crystal Structure Of Truncated Fibrobacter Succinogenes 1, 3-1, 4-Beta-D-Glucanase In Complex With Beta-1, 3-1, 4-Cellotriose
J. Mol. Biol. V. 354 642 2005
PubMed-ID: 16246371  |  Reference-DOI: 10.1016/J.JMB.2005.09.041
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GLUCANASE
    Chains: A, B
    EC Number: 3.2.1.73
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B(+)
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FRAGMENT 4-244
    Organism Scientific: FIBROBACTER SUCCINOGENES
    Organism Taxid: 833
    Synonym: ENDO-BETA-1,3-1,4 GLUCANASE, 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE, MIXED LINKAGE BETA- GLUCANASE, LICHENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2CA2Ligand/IonCALCIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:44 , ARG A:137 , TRP A:203 , THR A:204 , BGC A:301 , HOH A:548 , HOH A:550 , HOH A:555BINDING SITE FOR RESIDUE BGC A 300
2AC2SOFTWAREGLU A:11 , TYR A:42 , GLU A:47 , TRP A:54 , ARG A:137 , TRP A:203 , BGC A:300 , BGC A:302BINDING SITE FOR RESIDUE BGC A 301
3AC3SOFTWAREVAL A:36 , SER A:38 , PHE A:40 , TRP A:54 , GLU A:56 , GLU A:60 , ILE A:74 , ASN A:139 , TRP A:141 , BGC A:301 , HOH A:409 , HOH A:517BINDING SITE FOR RESIDUE BGC A 302
4AC4SOFTWAREASN B:44 , ARG B:137 , TRP B:203 , THR B:204 , BGC B:301 , HOH B:1409BINDING SITE FOR RESIDUE BGC B 300
5AC5SOFTWAREGLU B:11 , TYR B:42 , GLU B:47 , TRP B:203 , BGC B:300 , BGC B:302 , HOH B:1429 , HOH B:1497BINDING SITE FOR RESIDUE BGC B 301
6AC6SOFTWAREVAL B:36 , SER B:38 , PHE B:40 , TRP B:54 , GLU B:56 , ASP B:58 , GLU B:60 , ILE B:74 , ASN B:139 , TRP B:141 , BGC B:301 , HOH B:1565BINDING SITE FOR RESIDUE BGC B 302
7AC7SOFTWAREASN A:164 , ASN A:189 , GLY A:222 , HOH A:458 , HOH A:459 , HOH A:520BINDING SITE FOR RESIDUE CA A 400
8AC8SOFTWAREASN B:164 , ASN B:189 , GLY B:222 , HOH B:1426 , HOH B:1557BINDING SITE FOR RESIDUE CA B 1400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZM1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:91 -Pro A:92
2Leu A:157 -Pro A:158
3Ser B:91 -Pro B:92
4Leu B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZM1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH16_1PS01034 Glycosyl hydrolases family 16 active sites.GUB_FIBSS79-89
 		  2A:56-66
B:56-66

(-) Exons   (0, 0)

(no "Exon" information available for 1ZM1)

(-) 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:241
 aligned with GUB_FIBSS | P17989 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:241
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266 
            GUB_FIBSS    27 AKDFSGAELYTLEEVQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRDD 267
               SCOP domains d1zm1a_ A: Bacillus 1-3,1-4-beta-glucanase                                                                                                                                                                                                        SCOP domains
               CATH domains 1zm1A00 A:4-244  [code=2.60.120.200, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeeee......eeeeeeee.............eeeeeee.....eeeeeeeeee..eeee..eeee.........eeeeeee...eeeeee..eeeeeee.hhhhhh....eeeeeeee..hhhhhh..hhhhh.eeeeeeeeeeeee....hhhhh.eeeeeee.........eee.........eee....eeee..eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------GH16_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zm1 A   4 AKDFSGAELYTLEEVQYGKFEARmKmAAASGTVSSmFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGmLILALTRKGQESFNGQVPRDD 244
                                    13        23   | |  33     |  43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
                                                  27-MSE      39-MSE                                                                                                                                                                                 223-MSE                 
                                                    29-MSE                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with GUB_FIBSS | P17989 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:233
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
            GUB_FIBSS    27 AKDFSGAELYTLEEVQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGMLILALTRKGQESF 259
               SCOP domains d1zm1b_ B: Bacillus 1-3,1-4-beta-glucanase                                                                                                                                                                                                SCOP domains
               CATH domains 1zm1B00 B:4-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
           Pfam domains (1) Glyco_hydro_16-1zm1B01 B:4-167                                                                                                                                      --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_16-1zm1B02 B:4-167                                                                                                                                      --------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee..ee..eeeeeeee......eeeeeeee.............eeeeeee.....eeeeeeeeee..eee...eeee.........eeeeeee...eeeeee..eeeeeee.hhhhhh....eeeeeeee..hhhhhh..hhhhh.eeeeeeeeeeeee..........eeeeeee.........eee.........eee....eee....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------GH16_1     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zm1 B   4 AKDFSGAELYTLEEVQYGKFEARmKmAAASGTVSSmFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNRVDLTDKNIYSRDGmLILALTRKGQESF 236
                                    13        23   | |  33     |  43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
                                                  27-MSE      39-MSE                                                                                                                                                                                 223-MSE         
                                                    29-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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GUB_FIBSS | P17989)
molecular function
    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:0042972    licheninase activity    Catalysis of the hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3) and (1->4) bonds.
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/Swiss-Prot
        GUB_FIBSS | P17989: 1mve 2r49 3axd 3axe 3h0o 3hr9

(-) Related Entries Specified in the PDB File

1mve THE SAME PROTEIN COMPLEXED WITH BETA-1,3-1,4-CELLOTRIOSE