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(-) Description

Title :  CRYSTAL STRUCTURE OF CELD IN COMPLEX WITH AFFITIN E12
 
Authors :  A. Correa, S. Pacheco, A. E. Mechaly, G. Obal, G. Behar, B. Mouratou, P. O P. M. Alzari, F. Pecorari
Date :  18 Dec 13  (Deposition) - 21 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-De Novo Protein Complex, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Correa, S. Pacheco, A. E. Mechaly, G. Obal, G. Behar, B. Mouratou, P. Oppezzo, P. M. Alzari, F. Pecorari
Potent And Specific Inhibition Of Glycosidases By Small Artificial Binding Proteins (Affitins)
Plos One V. 9 97438 2014
PubMed-ID: 24823716  |  Reference-DOI: 10.1371/JOURNAL.PONE.0097438

(-) Compounds

Molecule 1 - ENDOGLUCANASE D
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15PREP4
    Expression System Taxid: 562
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: EGD, CELD, CELLULASE D, ENDO-1,4-BETA-GLUCANASE
 
Molecule 2 - E12 AFFITIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2GOL6Ligand/IonGLYCEROL
3ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:356 , SER A:358 , ASP A:361 , ASP A:362 , ASP A:401 , HOH A:2602 , HOH A:2603BINDING SITE FOR RESIDUE CA A1576
02AC2SOFTWAREGLU A:236 , ASN A:239 , ILE A:241 , ASP A:243 , ASP A:246 , HOH A:2458BINDING SITE FOR RESIDUE CA A1577
03AC3SOFTWARESER A:520 , ASP A:523 , ILE A:525 , HOH A:2776 , HOH A:2777 , HOH A:2778 , HOH A:2779BINDING SITE FOR RESIDUE CA A1578
04AC4SOFTWARECYS A:155 , CYS A:173 , HIS A:174 , HIS A:197BINDING SITE FOR RESIDUE ZN A1579
05AC5SOFTWAREASP A:397 , TYR A:456 , HOH A:2653 , ARG B:25 , ASN B:26 , LEU B:27 , HOH B:2011 , HOH B:2041 , HOH B:2042BINDING SITE FOR RESIDUE GOL B1067
06AC6SOFTWARELEU A:335 , ARG A:363 , ASP A:382 , ARG A:386 , HOH A:2566 , HOH A:2607 , HOH A:2819BINDING SITE FOR RESIDUE GOL A1580
07AC7SOFTWAREPRO A:172 , CYS A:173 , HIS A:174 , THR A:175 , PRO A:282 , GLU A:283 , GLU A:285 , HIS A:286 , HOH A:2331 , HOH A:2820BINDING SITE FOR RESIDUE GOL A1581
08AC8SOFTWAREPHE A:276 , TYR A:551 , TYR B:30 , HOH B:2043 , HOH B:2044BINDING SITE FOR RESIDUE GOL B1068
09AC9SOFTWAREASP A:201 , PHE A:276 , HIS A:516 , ARG A:518 , TYR A:551 , GLU A:555 , HOH A:2821 , LYS B:29 , TYR B:30BINDING SITE FOR RESIDUE GOL A1582
10BC1SOFTWAREASP A:399 , TRP A:400 , ASP A:401 , TYR A:456 , HOH A:2648 , HOH A:2658 , HOH A:2720 , LEU B:27BINDING SITE FOR RESIDUE GOL A1583

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CJ0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:177 -Ala A:178
2Trp A:538 -Pro A:539

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CJ0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F9_1PS00592 Glycosyl hydrolases family 9 active sites signature 1.GUND_CLOTM478-494  1A:502-518
2GLYCOSYL_HYDROL_F9_2PS00698 Glycosyl hydrolases family 9 active sites signature 2.GUND_CLOTM520-538  1A:544-562

(-) Exons   (0, 0)

(no "Exon" information available for 4CJ0)

(-) 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:534
 aligned with GUND_CLOTM | P0C2S4 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:534
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547    
           GUND_CLOTM    18 AKITENYQFDSRIRLNSIGFIPNHSKKATIAANCSTFYVVKEDGTIVYTGTATSMFDNDTKETVYIADFSSVNEEGTYYLAVPGVGKSVNFKIAMNVYEDAFKTAMLGMYLLRCGTSVSATYNGIHYSHGPCHTNDAYLDYINGQHTKKDSTKGWHDAGDYNKYVVNAGITVGSMFLAWEHFKDQLEPVALEIPEKNNSIPDFLDELKYEIDWILTMQYPDGSGRVAHKVSTRNFGGFIMPENEHDERFFVPWSSAATADFVAMTAMAARIFRPYDPQYAEKCINAAKVSYEFLKNNPANVFANQSGFSTGEYATVSDADDRLWAAAEMWETLGDEEYLRDFENRAAQFSKKIEADFDWDNVANLGMFTYLLSERPGKNPALVQSIKDSLLSTADSIVRTSQNHGYGRTLGTTYYWGCNGTVVRQTMILQVANKISPNNDYVNAALDAISHVFGRNYYNRSYVTGLGINPPMNPHDRRSGADGIWEPWPGYLVGGGWPGPKDWVDIQDSYQTNEIAINWNAALIYALAGFVNYN 551
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............ee....ee......eeee.....eeeeee....eeeeee.eeeee....eeeeeee.......eeeeeee...ee...eee....hhhhhhhhhhhhhhh.....eeeee..eeeee.........hhhhhh..................eehhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.............eee........hhhhh....ee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......................hhhhhhh..........................hhhhhh.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F-------------------------GLYCOSYL_HYDROL_F9_------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cj0 A  42 AKITENYQFDSRIRLNSIGFIPNHSKKATIAANCSTFYVVKEDGTIVYTGTATSMFDNDTKETVYIADFSSVNEEGTYYLAVPGVGKSVNFKIAMNVYEDAFKTAMLGMYLLRCGTSVSATYNGIHYSHGPCHTNDAYLDYINGQHTKKDSTKGWHDAGDYNKYVVNAGITVGSMFLAWEHFKDQLEPVALEIPEKNNSIPDFLDELKYEIDWILTMQYPDGSGRVAHKVSTRNFGGFIMPENEHDERFFVPWSSAATADFVAMTAMAARIFRPYDPQYAEKCINAAKVSYEFLKNNPANVFANQSGFSTGEYATVSDADDRLWAAAEMWETLGDEEYLRDFENRAAQFSKKIEADFDWDNVANLGMFTYLLSERPGKNPALVQSIKDSLLSTADSIVRTSQNHGYGRTLGTTYYWGCNGTVVRQTMILQVANKISPNNDYVNAALDAISHVFGRNYYNRSYVTGLGINPPMNPHDRRSGADGIWEPWPGYLVGGGWPGPKDWVDIQDSYQTNEIAINWNAALIYALAGFVNYN 575
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571    


Chain B from PDB  Type:PROTEIN  Length:60
                                                                                            
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeeeee....eeeeeee..eeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 4cj0 B   2 VKVKFVSSGEEKEVDTSKIKKVWRNLTKYGTIVQFTYDGRGYVRELDAPKELLDMLARAE  66
                                    11        21        31       |46        56        66
                                                                39|                     
                                                                 45
   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 4CJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CJ0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUND_CLOTM | P0C2S4)
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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GUND_CLOTM | P0C2S4: 1clc 4cj1

(-) Related Entries Specified in the PDB File

4cj1 CRYSTAL STRUCTURE OF CELD IN COMPLEX WITH AFFITIN H3
4cj2 CRYSTAL STRUCTURE OF HEWL IN COMPLEX WITH AFFITIN H4