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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE SPORULATION-SPECIFIC GLYCOSYLASE YDHD FROM BACILLUS SUBTILIS
 
Authors :  Y. Patskovsky, R. Romero, M. Rutter, S. Chang, M. Maletic, D. Smith, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx R Center For Structural Genomics (Nysgxrc)
Date :  28 Apr 08  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Uncharacterized Protein, Protein Structure Initiative, Psi-2, New York Sgx Research Center For Structural Genomics, Nysgxrc, Carbohydrate Metabolism, Glycosidase, Hydrolase, Polysaccharide Degradation, Sporulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Romero, M. Rutter, S. Chang, M. Maletic, D. Smith, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Glycosylase Ydhd From Bacillu Subtilis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SPORULATION-SPECIFIC GLYCOSYLASE YDHD
    Chains: A, B
    EC Number: 3.2.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 96-403
    Gene: YDHD, BSU05710
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Strain: 168 / JH642

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:124 , SER A:126 , SER A:127 , THR A:160BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWARELEU A:103 , PHE A:173 , ASP A:210 , GLU A:212 , LEU B:402BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWARETYR B:106 , SER B:126BINDING SITE FOR RESIDUE GOL B 503
4AC4SOFTWARELEU B:103 , PHE B:131 , GLU B:212 , TRP B:398BINDING SITE FOR RESIDUE GOL B 504
5AC5SOFTWAREILE A:339 , GLU A:375 , GLN B:336BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREGLN A:399 , THR A:401BINDING SITE FOR RESIDUE GOL A 506
7AC7SOFTWAREALA B:246 , MET B:273 , TYR B:275BINDING SITE FOR RESIDUE GOL B 507
8AC8SOFTWARESER B:126 , SER B:127 , TYR B:269BINDING SITE FOR RESIDUE GOL B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CZ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CZ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3CZ8)

(-) 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:302
 aligned with YDHD_BACSU | O05495 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:308
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
           YDHD_BACSU    96 SNYIAGTLSFYVLRNPDLDRELINDYAPYSSSISIFEYHIAPNGDIANQLNDAAAIETTWQRRVTPLATITNLTSGGFSTEIVHQVLNNPTARTNLVNNIYDLVSTRGYGGVTIDFEQVSAADRDLFTGFLRQLRDRLQAGGYVLTIAVPAKTSDNIPWLRGYDYGGIGAVVNYMFIMAYDWHHAGSEPGPVAPITEIRRTIEFTIAQVPSRKIIIGVPLYGYDWIIPYQPGTVASAISNQNAIERAMRYQAPIQYSAEYQSPFFRYSDQQGRTHEVWFEDVRSMSRKMQIVREYRLQAIGAWQLTLG 403
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.hhhh------........................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz8 A  96 SNYIAGTLSFYVLRNPDLD------YAPYSSSISIFEYHIAPNGDIANQLNDAAAIETTWQRRVTPLATITNLTSGGFSTEIVHQVLNNPTARTNLVNNIYDLVSTRGYGGVTIDFEQVSAADRDLFTGFLRQLRDRLQAGGYVLTIAVPAKTSDNIPWLRGYDYGGIGAVVNYMFIMAYDWHHAGSEPGPVAPITEIRRTIEFTIAQVPSRKIIIGVPLYGYDWIIPYQPGTVASAISNQNAIERAMRYQAPIQYSAEYQSPFFRYSDQQGRTHEVWFEGVRSMSRKMQIVREYRLQAIGAWQLTLA 403
                                   105        |-     | 125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
                                            114    121                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with YDHD_BACSU | O05495 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:308
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
           YDHD_BACSU    96 SNYIAGTLSFYVLRNPDLDRELINDYAPYSSSISIFEYHIAPNGDIANQLNDAAAIETTWQRRVTPLATITNLTSGGFSTEIVHQVLNNPTARTNLVNNIYDLVSTRGYGGVTIDFEQVSAADRDLFTGFLRQLRDRLQAGGYVLTIAVPAKTSDNIPWLRGYDYGGIGAVVNYMFIMAYDWHHAGSEPGPVAPITEIRRTIEFTIAQVPSRKIIIGVPLYGYDWIIPYQPGTVASAISNQNAIERAMRYQAPIQYSAEYQSPFFRYSDQQGRTHEVWFEDVRSMSRKMQIVREYRLQAIGAWQLTLG 403
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.hhhh----------....................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz8 B  96 SNYIAGTLSFYVLRNPDLD----------SSSISIFEYHIAPNGDIANQLNDAAAIETTWQRRVTPLATITNLTSGGFSTEIVHQVLNNPTARTNLVNNIYDLVSTRGYGGVTIDFEQVSAADRDLFTGFLRQLRDRLQAGGYVLTIAVPAKTSDNIPWLRGYDYGGIGAVVNYMFIMAYDWHHAGSEPGPVAPITEIRRTIEFTIAQVPSRKIIIGVPLYGYDWIIPYQPGTVASAISNQNAIERAMRYQAPIQYSAEYQSPFFRYSDQQGRTHEVWFEGVRSMSRKMQIVREYRLQAIGAWQLTLA 403
                                   105        |-       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
                                            114        125
   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  (0, 0)

(no "SCOP Domain" information available for 3CZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CZ8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YDHD_BACSU | O05495)
molecular function
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    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:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    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:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0031160    spore wall    The specialized envelope lying outside the cell membrane of a spore.

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