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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CELK CBM4 FROM CLOSTRIDIUM THERMOCELLUM
 
Authors :  P. M. Alahuhta, Y. Luo, V. V. Lunin
Date :  11 Oct 10  (Deposition) - 24 Aug 11  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Beta-Sandwich, Carbohydrate Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Alahuhta, Y. Luo, S. Y. Ding, M. E. Himmel, V. V. Lunin
Structure Of Cbm4 From Clostridium Thermocellum Cellulase K
Acta Crystallogr. , Sect. F V. 67 527 2011
PubMed-ID: 21543854  |  Reference-DOI: 10.1107/S1744309111003307

(-) Compounds

Molecule 1 - CELLULOSE 1,4-BETA-CELLOBIOSIDASE
    Chains: A, B
    EC Number: 3.2.1.91
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-210
    Gene: CELK
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4SO49Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL1Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:41 , ASP A:43 , ASN A:73 , LYS A:74 , ASP A:186 , HOH A:248BINDING SITE FOR RESIDUE CA A 205
02AC2SOFTWARESER A:27 , HOH A:244BINDING SITE FOR RESIDUE ACT A 206
03AC3SOFTWAREPRO A:129 , THR A:131 , THR B:131 , TYR B:159BINDING SITE FOR RESIDUE ACT A 207
04AC4SOFTWAREARG A:194 , HOH A:449BINDING SITE FOR RESIDUE ACT A 208
05AC5SOFTWARETRP A:88 , LYS A:122 , TYR A:130 , HIS A:170 , HOH A:300BINDING SITE FOR RESIDUE GOL A 209
06AC6SOFTWARELYS A:87 , ARG A:118 , GLU A:174BINDING SITE FOR RESIDUE SO4 A 210
07AC7SOFTWAREASN A:142 , HOH A:263 , ASN B:142 , GOL B:206BINDING SITE FOR RESIDUE SO4 A 211
08AC8SOFTWAREARG A:77BINDING SITE FOR RESIDUE SO4 A 212
09AC9SOFTWARELYS A:115 , ALA A:177 , GLY A:178 , HOH A:387 , LYS B:115 , SO4 B:209BINDING SITE FOR RESIDUE SO4 A 213
10BC1SOFTWARETHR B:41 , ASP B:43 , ASN B:73 , LYS B:74 , ASP B:186 , HOH B:236BINDING SITE FOR RESIDUE CA B 205
11BC2SOFTWARETHR A:144 , GLN A:147 , SO4 A:211 , ASN B:136 , PRO B:140 , PHE B:141 , ASN B:142 , HOH B:445BINDING SITE FOR RESIDUE GOL B 206
12BC3SOFTWARELYS B:87 , ARG B:118 , GLU B:174BINDING SITE FOR RESIDUE SO4 B 207
13BC4SOFTWAREARG B:77BINDING SITE FOR RESIDUE SO4 B 208
14BC5SOFTWARELYS A:115 , SO4 A:213 , LYS B:115 , ALA B:177 , GLY B:178 , HOH B:396BINDING SITE FOR RESIDUE SO4 B 209
15BC6SOFTWAREARG B:194 , HOH B:275 , HOH B:428BINDING SITE FOR RESIDUE SO4 B 210
16BC7SOFTWAREARG B:93 , ARG B:95BINDING SITE FOR RESIDUE SO4 B 211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P6B)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Phe A:48 -Pro A:49
2Glu A:128 -Pro A:129
3Thr A:179 -Pro A:180
4Leu A:203 -Pro A:204
5Phe B:48 -Pro B:49
6Glu B:128 -Pro B:129
7Thr B:179 -Pro B:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P6B)

(-) Exons   (0, 0)

(no "Exon" information available for 3P6B)

(-) 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:186
 aligned with CELK_CLOTM | P0C2S1 from UniProtKB/Swiss-Prot  Length:895

    Alignment length:186
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204      
           CELK_CLOTM    25 VFALEDKSSKLPDYKNDLLYERTFDEGLCFPWHTCEDSGGKCDFAVVDVPGEPGNKAFRLTVIDKGQNKWSVQMRHRGITLEQGHTYTVRFTIWSDKSCRVYAKIGQMGEPYTEYWNNNWNPFNLTPGQKLTVEQNFTMNYPTDDTCEFTFHLGGELAAGTPYYVYLDDVSLYDPRFVKPVEYVLP 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh...............eeee...eeeeeeeee.......eeeeeeeeee..hhh.eeeeeeeeee....eeeeeeeeee...eeeeeeeee......eee......eee...eeeeeeeeee.....eeeeeeeee.hhhhh....eeeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p6b A  19 HMALEDKSSKLPDYKNDLLYERTFDEGLCFPWHTCEDSGGKCDFAVVDVPGEPGNKAFRLTVIDKGQNKWSVQMRHRGITLEQGHTYTVRFTIWSDKSCRVYAKIGQMGEPYTEYWNNNWNPFNLTPGQKLTVEQNFTMNYPTDDTCEFTFHLGGELAAGTPYYVYLDDVSLYDPRFVKPVEYVLP 204
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198      


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with CELK_CLOTM | P0C2S1 from UniProtKB/Swiss-Prot  Length:895

    Alignment length:186
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204      
           CELK_CLOTM    25 VFALEDKSSKLPDYKNDLLYERTFDEGLCFPWHTCEDSGGKCDFAVVDVPGEPGNKAFRLTVIDKGQNKWSVQMRHRGITLEQGHTYTVRFTIWSDKSCRVYAKIGQMGEPYTEYWNNNWNPFNLTPGQKLTVEQNFTMNYPTDDTCEFTFHLGGELAAGTPYYVYLDDVSLYDPRFVKPVEYVLP 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhh...............eeee...eeeeeeeee.......eeeeeeeeee..hhh.eeeeeeeeee....eeeeeeeeee...eeeeeeeee......eee......eee...eeeeeeeeee.....eeeeeeeee.hhhhh....eeeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p6b B  19 HMALEDKSSKLPDYKNDLLYERTFDEGLCFPWHTCEDSGGKCDFAVVDVPGEPGNKAFRLTVIDKGQNKWSVQMRHRGITLEQGHTYTVRFTIWSDKSCRVYAKIGQMGEPYTEYWNNNWNPFNLTPGQKLTVEQNFTMNYPTDDTCEFTFHLGGELAAGTPYYVYLDDVSLYDPRFVKPVEYVLP 204
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
   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 3P6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P6B)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CELK_CLOTM | P0C2S1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    GO:0016162    cellulose 1,4-beta-cellobiosidase activity    Catalysis of the hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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(-) Related Entries Specified in the PDB File

3k4z CBHA CBM4 MODULE