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(-) Description

Title :  STRUCTURE OF FAE SOLVED BY SAD FROM DATA COLLECTED BY DIRECT DATA COLLECTION (DDC) USING THE GROB ROBOT GONIOMETER
 
Authors :  M. W. Bowler
Date :  04 Jan 13  (Deposition) - 01 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Ferrer, N. A. Larive, M. W. Bowler, D. Nurizzo
Recent Progress In Robot-Based Systems For Crystallography And Their Contribution To Drug Discovery.
Expert Opin. Drug Discov. V. 8 835 2013
PubMed-ID: 23656378  |  Reference-DOI: 10.1517/17460441.2013.793666

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE Y
    Atcc: 1515
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1094188
    Strain: YS
    Synonym: XYLANASE Y, 1,4-BETA-D-XYLAN XYLANOHYDROLASE Y, XYLY, FERULOYL ESTERASE DOMAIN

 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  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1CD12Ligand/IonCADMIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
3SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:823 , HIS A:886 , MSE A:889 , HOH A:3178 , GLU B:1017BINDING SITE FOR RESIDUE CD A2086
02AC2SOFTWAREGLU A:894 , HIS A:1076 , GLU A:1079 , HIS A:1083 , HIS A:1085BINDING SITE FOR RESIDUE CD A2087
03AC3SOFTWAREGLU A:1007 , HOH A:3290 , HOH A:3380 , HIS B:1082 , HIS B:1084BINDING SITE FOR RESIDUE CD A2088
04AC4SOFTWAREHIS A:947 , HIS A:1080 , HOH A:3233 , HOH A:3237 , HOH A:3238 , HOH A:3353BINDING SITE FOR RESIDUE CD A2089
05AC5SOFTWAREHIS A:1081 , HOH A:3382BINDING SITE FOR RESIDUE CD A2090
06AC6SOFTWAREGLU A:1017 , CYS B:823 , HIS B:886 , MSE B:889 , HOH B:3185BINDING SITE FOR RESIDUE CD B2086
07AC7SOFTWAREGLU B:894 , HIS B:1076 , GLU B:1079 , HIS B:1083 , HIS B:1085BINDING SITE FOR RESIDUE CD B2087
08AC8SOFTWAREHIS A:1082 , HIS A:1084 , GLU B:1007 , HOH B:3278 , HOH B:3279BINDING SITE FOR RESIDUE CD B2088
09AC9SOFTWAREHIS B:947 , HIS B:1080 , HOH B:3228 , HOH B:3232 , HOH B:3233 , HOH B:3347BINDING SITE FOR RESIDUE CD B2089
10BC1SOFTWAREHIS B:1081 , HOH B:3367BINDING SITE FOR RESIDUE CD B2090
11BC2SOFTWAREALA A:933 , HOH A:3217 , HOH A:3221 , HOH A:3225BINDING SITE FOR RESIDUE CD A2091
12BC3SOFTWAREGLU B:926 , TYR B:929 , HOH B:3212 , HOH B:3216BINDING SITE FOR RESIDUE CD B2091

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZI7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZI7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZI7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZI7)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZI7)

(-) 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 d3zi7a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee..........eeeeee...............hhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhh..............eeeeee.....hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3zi7 A  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLmHGGGENENTIFSNDVKLQNILDHAImNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRmHRGFGGFsmGGLTTWYVmVNCLDYVAYFmPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANmNPQIEAmKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 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   
                                                                                      863-MSE                   889-MSE                                                  946-MSE 954-SEP   964-MSE    975-MSE                                         1024-MSE  |                                                      
                                                                                                                                                                                  955-MSE                                                                    1031-MSE                                                  


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 d3zi7b_ B: Feruloyl esterase domain of the cellulosomal xylanase y                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee..........eeeeee...............hhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3zi7 B  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLmHGGGENENTIFSNDVKLQNILDHAImNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRmHRGFGGFsmGGLTTWYVmVNCLDYVAYFmPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANmNPQIEAmKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 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   
                                                                                      863-MSE                   889-MSE                                                  946-MSE 954-SEP   964-MSE    975-MSE                                         1024-MSE  |                                                      
                                                                                                                                                                                  955-MSE                                                                    1031-MSE
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZI7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZI7)

(-) 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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  3zi7
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  XYNY_CLOTM | P51584
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  3.2.1.8
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3zi6 STRUCTURE OF THERMOLYSIN SOLVED BY SAD FROM DATA COLLECTED BY DIRECT DATA COLLECTION (DDC) USING THE GROB ROBOT GONIOMETER