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(-) Description

Title :  S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH FERULIC ACID
 
Authors :  J. A. M. Prates, N. Tarbouriech, S. J. Charnock, C. M. G. A. Fontes, L. M. A. Ferreira, G. J. Davies
Date :  15 Aug 01  (Deposition) - 13 Dec 01  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Esterase Family 1, Inactive Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. M. Prates, N. Tarbouriech, S. J. Charnock, C. M. G. A. Fontes, L. M. A. Ferreira, G. J. Davies
The Structure Of The Feruloyl Esterase Module Of Xylanase 10B From Clostridium Thermocellum Provides Insights Into Substrate Recognition
Structure V. 9 1183 2001
PubMed-ID: 11738044

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE Y
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: FERULOYL ESTERASE DOMAIN
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Strain: YS
    Synonym: CBM22-2,XYLANASE Y, XYLY, 1,4-BETA-D-XYLAN XYLANOHYDROLASE Y

 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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD12Ligand/IonCADMIUM ION
3FER2Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOICACID
4GOL4Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOICACID
4GOL2Ligand/IonGLYCEROL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOICACID
4GOL2Ligand/IonGLYCEROL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:823 , HIS A:886 , MET A:889 , HOH A:2158 , GLU B:1017BINDING SITE FOR RESIDUE CD A3090
02AC2SOFTWAREGLU A:894 , HIS A:1076 , GLU A:1079 , HIS A:1083 , HIS A:1085BINDING SITE FOR RESIDUE CD A3091
03AC3SOFTWAREGLU A:1007 , HOH A:2259 , HIS B:1082 , HIS B:1084 , HOH B:2356BINDING SITE FOR RESIDUE CD A3092
04AC4SOFTWAREHIS A:947 , HIS A:1080 , HOH A:2215 , HOH A:2219 , HOH A:2326 , HOH A:2337BINDING SITE FOR RESIDUE CD A3093
05AC5SOFTWAREHIS A:1081 , HOH A:2341 , HOH A:2346 , CD A:3095BINDING SITE FOR RESIDUE CD A3094
06AC6SOFTWAREHIS A:1081 , HOH A:2370 , ACT A:3089 , CD A:3094BINDING SITE FOR RESIDUE CD A3095
07AC7SOFTWAREGLU A:1017 , CYS B:823 , HIS B:886 , MET B:889 , HOH B:2155BINDING SITE FOR RESIDUE CD B3090
08AC8SOFTWAREGLU B:894 , HIS B:1076 , GLU B:1079 , HIS B:1083 , HIS B:1085BINDING SITE FOR RESIDUE CD B3091
09AC9SOFTWAREHIS A:1082 , HIS A:1084 , HOH A:2344 , HOH A:2357 , GLU B:1007BINDING SITE FOR RESIDUE CD B3092
10BC1SOFTWAREHIS B:947 , HIS B:1080 , HOH B:2222 , HOH B:2223 , HOH B:2335 , HOH B:2348BINDING SITE FOR RESIDUE CD B3093
11BC2SOFTWAREHIS B:1081 , HOH B:2353 , HOH B:2354 , HOH B:2355 , CD B:3095BINDING SITE FOR RESIDUE CD B3094
12BC3SOFTWAREHIS B:1081 , HOH B:2353 , HOH B:2381 , ACT B:3089 , CD B:3094BINDING SITE FOR RESIDUE CD B3095
13BC4SOFTWAREALA A:954 , LEU A:958 , GLY A:979 , ASP A:980 , TRP A:982 , ALA A:1020 , HOH A:2364 , HOH A:2365 , GOL A:3087BINDING SITE FOR RESIDUE FER A3086
14BC5SOFTWAREALA B:954 , LEU B:958 , GLY B:979 , ASP B:980 , TRP B:982 , ALA B:1020 , ASN B:1023 , HOH B:2374 , HOH B:2375 , HOH B:2376 , HOH B:2377 , GOL B:3087BINDING SITE FOR RESIDUE FER B3086
15BC6SOFTWAREGLY A:865 , GLY A:866 , GLU A:868 , PHE A:953 , ALA A:954 , HIS A:1058 , HOH A:2364 , HOH A:2366 , FER A:3086BINDING SITE FOR RESIDUE GOL A3087
16BC7SOFTWARELYS A:856 , TYR A:857 , ASN A:858 , GLU A:894 , PRO A:895 , TYR A:932 , HIS A:1081 , HOH A:2367BINDING SITE FOR RESIDUE GOL A3088
17BC8SOFTWARELYS A:856 , TYR A:857 , HIS A:1081 , HOH A:2368 , HOH A:2369 , CD A:3095BINDING SITE FOR RESIDUE ACT A3089
18BC9SOFTWAREGLY B:865 , GLY B:866 , GLU B:868 , PHE B:953 , ALA B:954 , HIS B:1058 , HOH B:2127 , HOH B:2374 , HOH B:2378 , FER B:3086BINDING SITE FOR RESIDUE GOL B3087
19CC1SOFTWARESER A:927 , LYS A:928 , GLU B:926 , SER B:927 , LYS B:928 , TYR B:929 , SER B:930 , HOH B:2200 , HOH B:2201 , HOH B:2203 , HOH B:2208 , HOH B:2379BINDING SITE FOR RESIDUE GOL B3088
20CC2SOFTWARELYS B:856 , TYR B:857 , HIS B:1081 , HOH B:2112 , HOH B:2380 , HOH B:2381 , CD B:3095BINDING SITE FOR RESIDUE ACT B3089

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GKL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GKL)

(-) Exons   (0, 0)

(no "Exon" information available for 1GKL)

(-) 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:283
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:283
                                                                                                                                                                                                                                                                                                           1077        
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072    |    -   
          XYNY_CLOTM    803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFSMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSDHIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHE--------    -
               SCOP domains d1gkla_ A: Feruloyl esterase domain of the cellulosomal xylanase y                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gklA00 A:803-1085  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee..........eeeeee...............hhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhh..............eeeeee.....hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gkl A  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFAMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 1085
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082   


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:283
                                                                                                                                                                                                                                                                                                           1077        
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072    |    -   
          XYNY_CLOTM    803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFSMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSDHIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHE--------    -
               SCOP domains d1gklb_ B: Feruloyl esterase domain of the cellulosomal xylanase y                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gklB00 B:803-1085  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee..........eeeeee...............hhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh..............eeeeeeeeee.hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gkl B  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFAMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 1085
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GKL)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XYNY_CLOTM | P51584)
molecular function
    GO:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    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.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
cellular component
    GO:0043263    cellulosome    An extracellular multi-enzyme complex containing up to 11 different enzymes aligned on a non-catalytic scaffolding glycoprotein. Functions to hydrolyze cellulose.

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  1gkl
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  XYNY_CLOTM | P51584
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNY_CLOTM | P51584: 1dyo 1gkk 1h6x 1h6y 1ohz 1wb4 1wb5 1wb6 2ccl 2w5f 2wys 2wze 3zi7 4bag 4h35 5fxm

(-) Related Entries Specified in the PDB File

1dyo XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN
1gkk FERULOYL ESTERASE DOMAIN OF XYNY FROM CLOSTRIDIUM THERMOCELLUM
1h6x THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING
1h6y THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING