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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF A FAMILY GH18 CHITINASE FROM FERN, PETERIS RYUKYUENSIS
 
Authors :  N. Umemoto, T. Numata, T. Ohnuma, T. Fukamizo
Date :  15 Oct 14  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chitinase, Hydrolase, Carbohydrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kitaoku, N. Umemoto, T. Ohnuma, T. Numata, T. Taira, S. Sakuda, T. Fukamizo
A Class Iii Chitinase Without Disulfide Bonds From The Fern Pteris Ryukyuensis: Crystal Structure And Ligand-Binding Studies.
Planta V. 242 895 2015
PubMed-ID: 25998529  |  Reference-DOI: 10.1007/S00425-015-2330-4

(-) Compounds

Molecule 1 - CHITINASE A
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDIES 153-423)
    Gene: PRCHIA
    Organism Scientific: PTERIS RYUKYUENSIS
    Organism Taxid: 367335

 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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:131 , GLY A:132 , ALA A:133 , LEU A:134 , PHE A:371 , SER A:372 , ASP A:374 , HOH A:705BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWARELYS A:269 , SER A:275 , SER A:298 , VAL A:299 , ASP A:301 , HOH A:668BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWARETYR A:130 , ASP A:245 , GLN A:306 , TYR A:308 , PHE A:371 , HOH A:737 , HOH A:738BINDING SITE FOR RESIDUE ACT A 403
4AC4SOFTWAREHOH A:736 , HOH A:737 , HOH A:738 , HOH A:739 , HOH A:740 , HOH A:741BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWAREILE B:131 , GLY B:132 , ALA B:133 , LEU B:134 , PHE B:371 , SER B:372 , ASP B:374 , HOH B:638BINDING SITE FOR RESIDUE EDO B 401
6AC6SOFTWARELYS B:269 , SER B:275 , SER B:298 , VAL B:299 , ASP B:301 , HOH B:652BINDING SITE FOR RESIDUE EDO B 402
7AC7SOFTWARETYR B:130 , ASP B:245 , GLN B:306 , TYR B:308 , PHE B:371 , HOH B:733 , HOH B:737BINDING SITE FOR RESIDUE ACT B 403
8AC8SOFTWAREHOH B:733 , HOH B:734 , HOH B:735 , HOH B:736 , HOH B:737 , HOH B:738BINDING SITE FOR RESIDUE MG B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RL3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:156 -Phe A:157
2Phe A:371 -Ser A:372
3Ala B:156 -Phe B:157
4Phe B:371 -Ser B:372

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RL3)

(-) Exons   (0, 0)

(no "Exon" information available for 4RL3)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhh......eeeeeeeeee.............ee.......hhhhhhhhhhhh..eeeeeeeee.ee..ee......hhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh.ee..hhhhh....hhhhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhh....eeeeehhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rl3 A 125 KVFREYIGALYNGVQFTDVPINSGVTFHFILAFAIDYTSAAAATNGVFNIYWQNSVLTPAAVQAIKAQHSNVKVMVSLGGDTISGSPVQFTATSVSSWVANAVSSLTSLINQYHLDGIDIDYEHFDQVSTSTFVSCIGQLITQLKANNVISVASIAPFDGVESQYTALFGQYSSVIDLVNFQFYSYGAGTSASQYVSLYNTAASKYGGGAKVLASFSTGGVGPAPSTVLSACQQLKSSGTLPGIFIFSADGSYASSAKFQYEQQAQTLLTS 395
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394 


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhh......eeeeeeeeee.............ee.......hhhhhhhhhhhh..eeeeeeeee.ee..ee......hhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh.ee..hhhhh....hhhhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhh....eeeeehhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rl3 B 125 KVFREYIGALYNGVQFTDVPINSGVTFHFILAFAIDYTSAAAATNGVFNIYWQNSVLTPAAVQAIKAQHSNVKVMVSLGGDTISGSPVQFTATSVSSWVANAVSSLTSLINQYHLDGIDIDYEHFDQVSTSTFVSCIGQLITQLKANNVISVASIAPFDGVESQYTALFGQYSSVIDLVNFQFYSYGAGTSASQYVSLYNTAASKYGGGAKVLASFSTGGVGPAPSTVLSACQQLKSSGTLPGIFIFSADGSYASSAKFQYEQQAQTLLTS 395
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394
   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  (0, 0)

(no "SCOP Domain" information available for 4RL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RL3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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4pxv