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(-) Description

Title :  CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-1,4-XYLANASE II COMPLEXED WITH SUBSTRATE AND PRODUCTS
 
Authors :  A. Y. Kovalevsky, Q. Wan, P. Langan, L. Coates
Date :  15 Oct 12  (Deposition) - 08 Jan 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Xylanase Ii, Xylopentaose, Induced Fit Mechanism, Oxocarbenium Ion, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Wan, Q. Zhang, S. Hamilton-Brehm, K. Weiss, M. Mustyakimov, L. Coates, P. Langan, D. Graham, A. Kovalevsky
X-Ray Crystallographic Studies Of Family 11 Xylanase Michaelis And Product Complexes: Implications For The Catalytic Mechanism.
Acta Crystallogr. , Sect. D V. 70 11 2014
PubMed-ID: 24419374  |  Reference-DOI: 10.1107/S1399004713023626

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE 2
    Chains: A
    EC Number: 3.2.1.8
    Organism Scientific: TRICHODERMA REESEI
    Organism Taxid: 51453
    Synonym: XYLANASE 2, 1,4-BETA-D-XYLAN XYLANOHYDROLASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4XYP4Ligand/IonBETA-D-XYLOPYRANOSE
5XYS1Ligand/IonXYLOPYRANOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:44 , TYR A:73 , TYR A:88 , ARG A:122 , GLN A:136 , TRP A:138 , GLU A:177 , TYR A:179 , XYP A:402 , TRS A:406 , HOH A:1006 , HOH A:1147BINDING SITE FOR RESIDUE XYP A 401
2AC2SOFTWAREASN A:71 , TYR A:73 , TYR A:96 , TYR A:179 , XYP A:401 , XYS A:403 , HOH A:1147BINDING SITE FOR RESIDUE XYP A 402
3AC3SOFTWAREASN A:71 , TYR A:96 , XYP A:402 , HOH A:1170 , HOH A:1206BINDING SITE FOR RESIDUE XYS A 403
4AC4SOFTWARETRP A:18 , SER A:127 , ILE A:128 , XYP A:405 , HOH A:1095 , HOH A:1104 , HOH A:1138BINDING SITE FOR RESIDUE XYP A 404
5AC5SOFTWARETRP A:18 , TYR A:77 , PRO A:126 , SER A:127 , TYR A:171 , XYP A:404 , TRS A:406 , HOH A:1011 , HOH A:1014BINDING SITE FOR RESIDUE XYP A 405
6AC6SOFTWAREASN A:44 , TYR A:77 , GLU A:86 , ARG A:122 , PRO A:126 , XYP A:401 , XYP A:405 , HOH A:1183BINDING SITE FOR RESIDUE TRS A 406
7AC7SOFTWAREASN A:92 , PHE A:93 , HIS A:144 , HOH A:1096 , HOH A:1101 , HOH A:1108 , HOH A:1181BINDING SITE FOR RESIDUE CA A 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:52 -Pro A:53
2Asn A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HKW)

(-) 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:190
                                                                                                                                                                                                                              
               SCOP domains d4hkwa_ A: Xylanase II                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeeee...eeeeeeeee..........eeeeeee..eeeeeeeeeeeee......eeeeeeeeee......eeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkw A   1 xTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
                            |                                                                                                                                                                                             
                            1-PCA
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:82 - Pro A:83   [ RasMol ]  
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  XYN2_HYPJR | P36217
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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
        XYN2_HYPJR | P36217: 1enx 1red 1ree 1ref 1xyo 1xyp 2d97 2d98 2dfb 2dfc 3lgr 4hk8 4hk9 4hkl 4hko 4s2d 4s2f 4s2g 4s2h 4xpv 4xq4 4xqd 4xqw 5k7p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HKW)