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(-) Description

Title :  HIGH RESOLUTION STRUCTURE FOR FAMILY 3A CARBOHYDRATE BINDING MODULE FROM THE CIPA SCAFFOLDING OF CLOSTRIDIUM THERMOCELLUM
 
Authors :  O. Yaniv, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Date :  04 Sep 12  (Deposition) - 12 Sep 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sugar Binding Protein, Cellulosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Yaniv, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
High Resolution Structure Of The Family 3A Carbohydrate-Binding Module From The Mafor Scaffoldin Subunit Cipa Of Clostridium Thermocellum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CELLULOSOMAL-SCAFFOLDING PROTEIN A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: RIL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 368-519
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM ATCC 27405
    Organism Taxid: 203119
    Synonym: CELLULOSE-INTEGRATING PROTEIN A, CELLULOSOMAL GLYCOPROTEIN S1/SL, COHESIN

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:44 , ASP A:46 , THR A:122 , ASN A:125 , ASP A:126 , HOH A:2090BINDING SITE FOR RESIDUE CA A 153
2AC2SOFTWARETHR B:44 , ASP B:46 , THR B:122 , ASN B:125 , ASP B:126 , HOH B:2199BINDING SITE FOR RESIDUE CA B 153
3AC3SOFTWAREARG A:40 , HOH A:2168 , SER B:35 , LYS B:36 , ASN B:146 , HOH B:2049 , HOH B:2051 , HOH B:2055 , HOH B:2198BINDING SITE FOR RESIDUE SO4 B1153
4AC4SOFTWARELYS B:49 , ASP B:50 , HOH B:2080BINDING SITE FOR RESIDUE SO4 B1154
5AC5SOFTWAREGLY B:62 , SER B:63 , ASN B:64 , GLY B:65 , SER B:66 , ASN B:68BINDING SITE FOR RESIDUE SO4 B1155
6AC6SOFTWARETYR A:67 , GLY A:69 , HOH A:2124 , HOH A:2140 , HOH A:2228 , HOH A:2230 , TRP B:118BINDING SITE FOR RESIDUE SO4 A1153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B9F)

(-) Exons   (0, 0)

(no "Exon" information available for 4B9F)

(-) 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:152
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:152
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517  
           CIPA_CLOTH   368 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWG 519
               SCOP domains d4b9fa_ A: Cellusomal scaffolding protein A, scaffoldin                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....ee....eeeeeee.....ee...eeeeeee.......eeeeeeeeeee.....eee....eeeeeeeeeeee..eeeeeeeee...ee....eeeeeeeeee.....ee.............ee....eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9f A   1 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWG 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:152
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517  
           CIPA_CLOTH   368 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWG 519
               SCOP domains d4b9fb_ B: Cellusomal scaffolding protein A, scaffoldin                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....ee....eeeeeee.....ee...eeeeeee.......eeeeeeeeeee.....eee....eeeeeeeeeeee..eeeeeeeee...ee....eeeeeeeeee.....ee.............ee....eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9f B   1 NLKVEFYNSNPSDTTNSINPQFKVTNTGSSAIDLSKLTLRYYYTVDGQKDQTFWCDHAAIIGSNGSYNGITSNVKGTFVKMSSSTNNADTYLEISFTGGTLEPGAHVQIQGRFAKNDWSNYTQSNDYSFKSASQFVEWDQVTAYLNGVLVWG 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (0, 0)

(no "CATH Domain" information available for 4B9F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B9F)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CIPA_CLOTH | Q06851)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.

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  4b9f
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  CIPA_CLOTH | Q06851
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 Related Entries

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

UniProtKB/Swiss-Prot
        CIPA_CLOTH | Q06851: 1anu 1aoh 1nbc 1ohz 2b59 2ccl 3kcp 5g5d

(-) Related Entries Specified in the PDB File

1anu COHESIN-2 DOMAIN OF THE CELLULOSOME FROM CLOSTRIDIUM THERMOCELLUM
1aoh SINGLE COHESIN DOMAIN FROM THE SCAFFOLDING PROTEIN CIPA OFTHE CLOSTRIDIUM THERMOCELLUM CELLULOSOME
1nbc BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN
1ohz COHESIN-DOCKERIN COMPLEX FROM THE CELLULOSOME OF CLOSTRIDIUM THERMOCELLUM
2b59 THE TYPE II COHESIN DOCKERIN COMPLEX
2ccl THE S45A, T46A MUTANT OF THE TYPE I COHESIN-DOCKERIN COMPLEX FROM THE CELLULOSOME OF CLOSTRIDIUM THERMOCELLUM