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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ACTIVE FORM CHITOSANASE FROM BACILLUS SP. K17 AT PH6.4
 
Authors :  W. Adachi, S. Shimizu, T. Sunami, T. Fukazawa, M. Suzuki, R. Yatsunami, S. Nakamura, A. Takenaka
Date :  22 Nov 03  (Deposition) - 07 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chitosan Degradation, Hydrolase, Glycosil Hydrolase, Family 8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Adachi, Y. Sakihama, S. Shimizu, T. Sunami, T. Fukazawa, M. Suzuki, R. Yatsunami, S. Nakamura, A. Takenaka
Crystal Structure Of Family Gh-8 Chitosanase With Subclass Ii Specificity From Bacillus Sp. K17
J. Mol. Biol. V. 343 785 2004
PubMed-ID: 15465062  |  Reference-DOI: 10.1016/J.JMB.2004.08.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITOSANASE
    Chains: A, B
    EC Number: 3.2.1.132
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 1409
    Strain: K17

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PIN1Ligand/IonPIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PIN-1Ligand/IonPIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PIN1Ligand/IonPIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:353 , SER A:370 , ASN A:371 , HOH A:1316 , TYR B:375 , HOH B:1135 , HOH B:1781 , HOH B:1930 , HOH B:1942BINDING SITE FOR RESIDUE PIN B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V5D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:55 -Pro A:56
2Asn A:297 -Pro A:298
3Phe B:55 -Pro B:56
4Asn B:297 -Pro B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V5D)

(-) Exons   (0, 0)

(no "Exon" information available for 1V5D)

(-) 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:386
 aligned with Q9ALZ1_9BACI | Q9ALZ1 from UniProtKB/TrEMBL  Length:453

    Alignment length:386
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428      
         Q9ALZ1_9BACI    49 AKEMKPFPQQVNYAGVIKPNHVTQESLNASVRSYYDNWKKKYLKNDLSSLPGGYYVKGEITGDADGFKPLGTSEGQGYGMIITVLMAGYDSNAQKIYDGLFKTARTFKSSQNPNLMGWVVADSKKAQGHFDSATDGDLDIAYSLLLAHKQWGSNGTVNYLKEAQDMITKGIKASNVTNNNRLNLGDWDSKSSLDTRPSDWMMSHLRAFYEFTGDKTWLTVINNLYDVYTQFSNKYSPNTGLISDFVVKNPPQPAPKDFLEESEYTNAYYYNASRVPLRIVMDYAMYGEKRSKVISDKVSSWIQNKTNGNPSKIVDGYQLNGSNIGSYSTAVFVSPFIAASITSSNNQKWVNSGWDWMKNKRESYFSDSYNLLTMLFITGNWWKPVP 434
               SCOP domains d1v5da_ A: Chitosanase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhee..........ee..............eehhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...........ee..hhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........ee....ee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...............hhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5d A  49 AKEMKPFPQQVNYAGVIKPNHVTQESLNASVRSYYDNWKKKYLKNDLSSLPGGYYVKGEITGDADGFKPLGTSEGQGYGMIITVLMAGYDSNAQKIYDGLFKTARTFKSSQNPNLMGWVVADSKKAQGHFDSATDGDLDIAYSLLLAHKQWGSNGTVNYLKEAQDMITKGIKASNVTNNNQLNLGDWDSKSSLDTRPSDWMMSHLRAFYEFTGDKTWLTVINNLYDVYTQFSNKYSPNTGLISDFVVKNPPQPAPKDFLDESEYTNAYYYNASRVPLRIVMDYAMYGEKRSKVISDKVSSWIQNKTNGNPSKIVDGYQLNGSNIGSYPTAVFVSPFIAASITSSNNQKWVNSGWDWMKNKRERYFSDSYNLLTMLFITGNWWKPVP 434
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428      


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q9ALZ1_9BACI | Q9ALZ1 from UniProtKB/TrEMBL  Length:453

    Alignment length:386
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428      
         Q9ALZ1_9BACI    49 AKEMKPFPQQVNYAGVIKPNHVTQESLNASVRSYYDNWKKKYLKNDLSSLPGGYYVKGEITGDADGFKPLGTSEGQGYGMIITVLMAGYDSNAQKIYDGLFKTARTFKSSQNPNLMGWVVADSKKAQGHFDSATDGDLDIAYSLLLAHKQWGSNGTVNYLKEAQDMITKGIKASNVTNNNRLNLGDWDSKSSLDTRPSDWMMSHLRAFYEFTGDKTWLTVINNLYDVYTQFSNKYSPNTGLISDFVVKNPPQPAPKDFLEESEYTNAYYYNASRVPLRIVMDYAMYGEKRSKVISDKVSSWIQNKTNGNPSKIVDGYQLNGSNIGSYSTAVFVSPFIAASITSSNNQKWVNSGWDWMKNKRESYFSDSYNLLTMLFITGNWWKPVP 434
               SCOP domains d1v5db_ B: Chitosanase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Glyco_hydro_8-1v5dB01 B:53-427                                                                                                                                                                                                                                                                                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ----Glyco_hydro_8-1v5dB02 B:53-427                                                                                                                                                                                                                                                                                                                                                         ------- Pfam domains (2)
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhee..........ee..............eehhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...........ee..hhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........ee....ee...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...............hhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5d B  49 AKEMKPFPQQVNYAGVIKPNHVTQESLNASVRSYYDNWKKKYLKNDLSSLPGGYYVKGEITGDADGFKPLGTSEGQGYGMIITVLMAGYDSNAQKIYDGLFKTARTFKSSQNPNLMGWVVADSKKAQGHFDSATDGDLDIAYSLLLAHKQWGSNGTVNYLKEAQDMITKGIKASNVTNNNQLNLGDWDSKSSLDTRPSDWMMSHLRAFYEFTGDKTWLTVINNLYDVYTQFSNKYSPNTGLISDFVVKNPPQPAPKDFLDESEYTNAYYYNASRVPLRIVMDYAMYGEKRSKVISDKVSSWIQNKTNGNPSKIVDGYQLNGSNIGSYPTAVFVSPFIAASITSSNNQKWVNSGWDWMKNKRERYFSDSYNLLTMLFITGNWWKPVP 434
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V5D)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9ALZ1_9BACI | Q9ALZ1)
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: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.

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 Related Entries

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

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        Q9ALZ1_9BACI | Q9ALZ1: 1v5c

(-) Related Entries Specified in the PDB File

1v5c THE SAME PROTEIN, THE INACTIVE FORM AT PH3.7