Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  NATIVE STRUCTURE OF ENDOGLUCANASE 12A (CEL12A) FROM RHODOTHERMUS MARINUS
 
Authors :  S. J. Crennell, E. Nordberg-Karlsson
Date :  13 Jul 05  (Deposition) - 21 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Endoglucanase, Cellulase, Glycoside Hydrolase Family 12 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Crennell, D. Cook, A. Minns, D. Svergun, R. L. Andersen, E. Nordberg-Karlsson
Dimerisation And An Increase In Active Site Aromatic Groups As Adaptations To High Temperatures: X-Ray Solution Scattering And Substrate-Bound Crystal Structures Of Rhodothermus Marinus Endoglucanase Cel12A.
J. Mol. Biol. V. 356 57 2006
PubMed-ID: 16343530  |  Reference-DOI: 10.1016/J.JMB.2005.11.004

(-) Compounds

Molecule 1 - ENDOGLUCANASE
    Chains: A, B
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: (SP, L)CEL12A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Organism Scientific: RHODOTHERMUS MARINUS
    Organism Taxid: 29549
    Other Details: MARINE THERMOPHILIC EUBACTERIUM ISOLATED FROM ALKALINE SUBMARINE HOT SPRINGS
    Strain: ITI-378

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:113 , ASN A:114 , ARG A:190 , HOH A:2121 , HOH A:2210 , HOH A:2211 , HOH A:2212 , HOH A:2213BINDING SITE FOR RESIDUE SO4 A1228

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:6 -A:33
2A:66 -A:71
3B:6 -B:33
4B:66 -B:71

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:77 -Pro A:78
2Leu B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BW8)

(-) Exons   (0, 0)

(no "Exon" information available for 2BW8)

(-) 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:226
 aligned with O33897_RHOMR | O33897 from UniProtKB/TrEMBL  Length:260

    Alignment length:226
                                                                                                                  125                                                                                                                                         
                                                                                                                124 |                                                                                                                                    260  
                                    47        57        67        77        87        97       107       117      |126       136       146       156       166       176       186       196       206       216       226       236       246       256   |  
         O33897_RHOMR    38 TVELCGRWDARDVAGGRYRVINNVWGAETAQCIEVGLETGNFTITRADHDNGNNVAAYPAIYFGCHWAPARAIRDCAARAGAVRRAH-ELDVTPITTGRWNAAYDIWFSPVTNSGNGYSGGAELMIWLNWNGGVMPGGSRVATVELAGATWEVWYADWDWNYIAYRRTTPTTSVSELDLKAFIDDAVARGYIRPEWYLHAVETGFELWEGGAGLRTADFSVTVQ--   -
               SCOP domains d2bw8a_ A: Family 12 endo-1,4-beta-glucanase (cellulase) catalytic domain                                                                                                                                                          SCOP domains
               CATH domains 2bw8A00 A:2-227  [code=2.60.120.180, no name defined]                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee....eeee.........eeeee......eeeeee............eeeeeee..ee............eeeeeeeeeee.....eeeeeeeeeee............eeeeeeeeee.......eeeeeeee..eeeeeeeee...eeeeeee.....eeeeeehhhhhhhhhhh.......eeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bw8 A   2 TVELCGRWDARDVAGGRYRVINNVWGAETAQCIEVGLETGNFTITRADHDNGNNVAAYPAIYFGCHWGACTSNSGLPRRVQELSDVRTSWTLTPITTGRWNAAYDIWFSPVTNSGNGYSGGAELMIWLNWNGGVMPGGSRVATVELAGATWEVWYADWDWNYIAYRRTTPTTSVSELDLKAFIDDAVARGYIRPEWYLHAVETGFELWEGGAGLRSADFSVTVQKL 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with O33897_RHOMR | O33897 from UniProtKB/TrEMBL  Length:260

    Alignment length:226
                                                                                                                  125                                                                                                                                         
                                                                                                                124 |                                                                                                                                    260  
                                    47        57        67        77        87        97       107       117      |126       136       146       156       166       176       186       196       206       216       226       236       246       256   |  
         O33897_RHOMR    38 TVELCGRWDARDVAGGRYRVINNVWGAETAQCIEVGLETGNFTITRADHDNGNNVAAYPAIYFGCHWAPARAIRDCAARAGAVRRAH-ELDVTPITTGRWNAAYDIWFSPVTNSGNGYSGGAELMIWLNWNGGVMPGGSRVATVELAGATWEVWYADWDWNYIAYRRTTPTTSVSELDLKAFIDDAVARGYIRPEWYLHAVETGFELWEGGAGLRTADFSVTVQ--   -
               SCOP domains d2bw8b_ B: Family 12 endo-1,4-beta-glucanase (cellulase) catalytic domain                                                                                                                                                          SCOP domains
               CATH domains 2bw8B00 B:2-227  [code=2.60.120.180, no name defined]                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee....eeee.........eeeee......eeeeee............eeeeeee..ee............eeeeeeeeeee.....eeeeeeeeeee............eeeeeeeeee.......eeeeeeee..eeeeeeeee...eeeeeee.....eeeeeehhhhhhhhhhh.......eeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bw8 B   2 TVELCGRWDARDVAGGRYRVINNVWGAETAQCIEVGLETGNFTITRADHDNGNNVAAYPAIYFGCHWGACTSNSGLPRRVQELSDVRTSWTLTPITTGRWNAAYDIWFSPVTNSGNGYSGGAELMIWLNWNGGVMPGGSRVATVELAGATWEVWYADWDWNYIAYRRTTPTTSVSELDLKAFIDDAVARGYIRPEWYLHAVETGFELWEGGAGLRSADFSVTVQKL 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BW8)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O33897_RHOMR | O33897)
molecular function
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal 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.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:77 - Pro A:78   [ RasMol ]  
    Leu B:77 - Pro B:78   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bw8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O33897_RHOMR | O33897
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  O33897_RHOMR | O33897
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O33897_RHOMR | O33897: 1h0b 2bwa 2bwc 3b7m

(-) Related Entries Specified in the PDB File

1h0b ENDOGLUCANASE CEL12A FROM RHODOTHERMUS MARINUS
2bwa STRUCTURE OF ENDOGLUCANASE 12A (CEL12A) FROM RHODOTHERMUS MARINUS IN COMPLEX WITH CELLOPENTAOSE, 20 MINUTE SOAK.
2bwc STRUCTURE OF ENDOGLUCANASE 12A (CEL12A) FROM RHODOTHERMUS MARINUS IN COMPLEX WITH CELLOPENTAOSE (5 MINUTE SOAK)