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(-) Description

Title :  CRYSTAL STRUCTURE OF CHITINASE C FROM STREPTOMYCES GRISEUS HUT6037
 
Authors :  Y. Kezuka, T. Watanabe, T. Nonaka
Date :  27 Dec 04  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Family 19 Chitinase, Whole Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kezuka, M. Ohishi, Y. Itoh, J. Watanabe, M. Mitsutomi, T. Watanabe, T. Nonaka
Structural Studies Of A Two-Domain Chitinase From Streptomyces Griseus Hut6037
J. Mol. Biol. V. 358 472 2006
PubMed-ID: 16516924  |  Reference-DOI: 10.1016/J.JMB.2006.02.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE C
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET12A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 30-294
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Synonym: GLYCOSYL HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1CL13Ligand/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  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:145 , HIS A:146 , LYS A:276 , GLN B:279BINDING SITE FOR RESIDUE CL A 295
02AC2SOFTWAREILE B:154 , LYS B:155 , HOH B:339BINDING SITE FOR RESIDUE CL B 295
03AC3SOFTWAREARG B:105 , THR B:110 , TYR B:111 , HOH B:379BINDING SITE FOR RESIDUE CL B 296
04AC4SOFTWAREGLU A:159 , LYS A:222BINDING SITE FOR RESIDUE CL A 296
05AC5SOFTWAREASN A:275 , ASN B:104BINDING SITE FOR RESIDUE CL A 297
06AC6SOFTWARETYR A:121 , PRO A:122 , ALA A:123BINDING SITE FOR RESIDUE CL A 298
07AC7SOFTWAREARG A:105 , THR A:110 , TYR A:111 , HOH A:360BINDING SITE FOR RESIDUE CL A 299
08AC8SOFTWARELYS A:155 , ASP A:216 , PRO A:217 , ALA A:218BINDING SITE FOR RESIDUE CL A 300
09AC9SOFTWARETHR B:287 , THR B:288BINDING SITE FOR RESIDUE CL B 297
10BC1SOFTWAREGLN B:178 , GLY B:203 , HOH B:337BINDING SITE FOR RESIDUE CL B 298
11BC2SOFTWAREGLN A:178 , GLY A:203 , HOH A:350BINDING SITE FOR RESIDUE CL A 301
12BC3SOFTWAREASN A:266 , ASN B:266 , GLN B:269BINDING SITE FOR RESIDUE CL A 302
13BC4SOFTWARETYR B:121 , PRO B:122 , ALA B:123 , HOH B:318BINDING SITE FOR RESIDUE CL B 299

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:166 -A:174
2A:262 -A:294
3B:32 -B:78
4B:166 -B:174
5B:262 -B:294

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WVU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WVU)

(-) 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:209
 aligned with O50152_STRGR | O50152 from UniProtKB/TrEMBL  Length:294

    Alignment length:209
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         
         O50152_STRGR    86 GGNNGFVVSEAQFNQMFPNRNAFYTYKGLTDALSAYPAFAKTGSDEVKKREAAAFLANVSHETGGLFYIKEVNEANYPHYCDTTQSYGCPAGQAAYYGRGPIQLSWNFNYKAAGDALGINLLANPYLVEQDPAVAWKTGLWYWNSQNGPGTMTPHNAIVNNAGFGETIRSINGALECNGGNPAQVQSRINKFTQFTQILGTTTGPNLSC 294
               SCOP domains d1wvua_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------1wvuA02 A:155-215 Endochitinase, domain 2                    ------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh........................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvu A  86 GGNNGFVVSEAQFNQMFPNRNAFYTYKGLTDALSAYPAFAKTGSDEVKKREAAAFLANVSHETGGLFYIKEVNEANYPHYCDTTQSYGCPAGQAAYYGRGPIQLSWNFNYKAAGDALGINLLANPYLVEQDPAVAWKTGLWYWNSQNGPGTMTPHNAIVNNAGFGETIRSINGALECNGGNPAQVQSRINKFTQFTQILGTTTGPNLSC 294
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with O50152_STRGR | O50152 from UniProtKB/TrEMBL  Length:294

    Alignment length:263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         O50152_STRGR    32 CATAWSSSSVYTNGGTVSYNGRNYTAKWWTQNERPGTSDVWADKGACGTGGEGPGGNNGFVVSEAQFNQMFPNRNAFYTYKGLTDALSAYPAFAKTGSDEVKKREAAAFLANVSHETGGLFYIKEVNEANYPHYCDTTQSYGCPAGQAAYYGRGPIQLSWNFNYKAAGDALGINLLANPYLVEQDPAVAWKTGLWYWNSQNGPGTMTPHNAIVNNAGFGETIRSINGALECNGGNPAQVQSRINKFTQFTQILGTTTGPNLSC 294
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -CBM_5_12-1wvuB03 B:33-72                -------------------Glyco_hydro_19-1wvuB01 B:92-294                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------Glyco_hydro_19-1wvuB02 B:92-294                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author .........ee....eeee..eeeee...ee.........eeeeee..----------....hhhhhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh........................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wvu B  32 CATAWSSSSVYTNGGTVSYNGRNYTAKWWTQNERPGTSDVWADKGACG----------GFVVSEAQFNQMFPNRNAFYTYKGLTDALSAYPAFAKTGSDEVKKREAAAFLANVSHETGGLFYIKEVNEANYPHYCDTTQSYGCPAGQAAYYGRGPIQLSWNFNYKAAGDALGINLLANPYLVEQDPAVAWKTGLWYWNSQNGPGTMTPHNAIVNNAGFGETIRSINGALECNGGNPAQVQSRINKFTQFTQILGTTTGPNLSC 294
                                    41        51        61        71       | -        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                          79         90
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: Lysozyme (266)
(-)
Clan: no clan defined [family: CBM_5_12] (10)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O50152_STRGR | O50152)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/TrEMBL
        O50152_STRGR | O50152: 1wvv 2d49 2dbt

(-) Related Entries Specified in the PDB File

1wvv THE SAME PROTEIN(E147Q)