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(-) Description

Title :  CRYSTAL STRUCTURE OF BRASSICA JUNCEA CHITINASE CATALYTIC MODULE GLU234ALA MUTANT (BJCHI3-E234A)
 
Authors :  W. Ubhayasekera, T. Bergfors, S. L. Mowbray
Date :  02 Jun 07  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chitinase, Endochitinase, Family 19, Conformational Changes, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ubhayasekera, C. M. Tang, S. W. T. Ho, G. Berglund, T. Bergfors, M. -L. Chye, S. L. Mowbray
Crystal Structures Of A Family 19 Chitinase From Brassica Juncea Show Flexibility Of Binding Cleft Loops
Febs J. V. 274 3695 2007
PubMed-ID: 17608716  |  Reference-DOI: 10.1111/J.1742-4658.2007.05906.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: KM71
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC MODULE, UNP RESIDUES 146-389
    Gene: BJCHI1
    Mutation: YES
    Organism Scientific: BRASSICA JUNCEA
    Organism Taxid: 3707

 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, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1CL19Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE B:256 , ARG B:260BINDING SITE FOR RESIDUE CL B 1001
02AC2SOFTWARELYS B:232 , GLU B:233 , HOH B:1104BINDING SITE FOR RESIDUE CL B 1002
03AC3SOFTWARELYS A:255 , PHE A:256 , ARG A:260BINDING SITE FOR RESIDUE CL A 1003
04AC4SOFTWAREHOH A:1153 , ARG B:153BINDING SITE FOR RESIDUE CL B 1004
05AC5SOFTWARELYS B:255 , ASN B:285 , ASP B:287BINDING SITE FOR RESIDUE CL B 1005
06AC6SOFTWAREGLY A:377BINDING SITE FOR RESIDUE CL A 1006
07AC7SOFTWARESER A:218 , GLY B:219 , GLY B:223 , ALA B:224 , HOH B:1088BINDING SITE FOR RESIDUE CL B 1007
08AC8SOFTWARELYS B:311 , GLY B:346 , GLY B:347 , ASN B:389 , HOH B:1170BINDING SITE FOR RESIDUE CL B 1008
09AC9SOFTWAREARG B:153 , TYR B:157 , TYR B:176 , ASP B:177BINDING SITE FOR RESIDUE CL B 1009
10BC1SOFTWAREGLU A:349 , CYS A:350 , ALA A:351 , GLY A:352 , ASP A:383 , HOH A:1088BINDING SITE FOR RESIDUE CL A 1010
11BC2SOFTWAREARG A:153 , TYR A:157 , TYR A:176 , ASP A:177BINDING SITE FOR RESIDUE CL A 1011
12BC3SOFTWAREASN A:225 , SER A:363 , HOH A:1113BINDING SITE FOR RESIDUE CL A 1012
13BC4SOFTWAREGLY A:145 , ALA A:183 , PHE A:186 , PRO A:187 , PHE A:189 , ASN A:191BINDING SITE FOR RESIDUE CL A 1013
14BC5SOFTWAREASP A:381 , CYS A:382 , ASN A:384 , GLN A:385 , HOH A:1118 , HOH A:1188BINDING SITE FOR RESIDUE CL A 1014
15BC6SOFTWAREGLU B:281 , LEU B:283 , LYS B:284 , HOH B:1194BINDING SITE FOR RESIDUE CL B 1015
16BC7SOFTWAREASP A:375 , HOH A:1222BINDING SITE FOR RESIDUE CL A 1016
17BC8SOFTWAREARG B:153 , TYR B:157BINDING SITE FOR RESIDUE CL B 1017
18BC9SOFTWARESER B:266 , ASN B:270BINDING SITE FOR RESIDUE CL B 1018
19CC1SOFTWARELYS B:237BINDING SITE FOR RESIDUE CL B 1019

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:168 -A:230
2A:242 -A:251
3A:350 -A:382
4B:168 -B:230
5B:242 -B:251
6B:350 -B:382

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:309 -Pro A:310
2Ala B:309 -Pro B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z39)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z39)

(-) 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:246
 aligned with Q9SQF7_BRAJU | Q9SQF7 from UniProtKB/TrEMBL  Length:400

    Alignment length:246
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
         Q9SQF7_BRAJU   144 SGDLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEEIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
               SCOP domains d2z39a_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 2z39A01 A:144-232,A:292-389  [code=1.10.530.10, no name defined]                         2z39A02 A:233-291 Endochitinase, domain 2                  2z39A01 A:144-232,A:292-389  [code=1.10.530.10, no name defined]                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh.......................................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z39 A 144 FGDLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEAIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      


Chain B from PDB  Type:PROTEIN  Length:244
 aligned with Q9SQF7_BRAJU | Q9SQF7 from UniProtKB/TrEMBL  Length:400

    Alignment length:244
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385    
         Q9SQF7_BRAJU   146 DLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEEIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
               SCOP domains d2z39b_ B: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 2z39B01 B:146-232,B:292-389  [code=1.10.530.10, no name defined]                       2z39B02 B:233-291 Endochitinase, domain 2                  2z39B01 B:146-232,B:292-389  [code=1.10.530.10, no name defined]                                   CATH domains
           Pfam domains (1) ----Glyco_hydro_19-2z39B01 B:150-382                                                                                                                                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ----Glyco_hydro_19-2z39B02 B:150-382                                                                                                                                                                                                         ------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhh..............hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.........hhhhh.......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z39 B 146 DLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEAIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9SQF7_BRAJU | Q9SQF7)
molecular function
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9SQF7_BRAJU | Q9SQF7: 2z37 2z38

(-) Related Entries Specified in the PDB File

2z37 BRASSICA JUNCEA CHITINASE CATALYTIC MODULE
2z38 BRASSICA JUNCEA CHITINASE CATALYTIC MODULE WITH BOUND CHLORIDE IONS