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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAMILY GH-19 CHITINASE FROM RYE SEEDS IN COMPLEX WITH (GLCNAC)4
 
Authors :  T. Numata, N. Umemoto, T. Ohnuma, T. Fukamizo
Date :  29 Feb 12  (Deposition) - 15 Aug 12  (Release) - 26 Jun 13  (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, Hydrolase, Carbohydrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ohnuma, T. Numata, T. Osawa, H. Inanaga, Y. Okazaki, S. Shinya, K. Kondo, T. Fukuda, T. Fukamizo
Crystal Structure And Chitin Oligosaccharide-Binding Mode O A 'Loopful' Family Gh19 Chitinase From Rye, Secale Cereale, Seeds
Febs J. V. 279 3639 2012
PubMed-ID: 22831795  |  Reference-DOI: 10.1111/J.1742-4658.2012.08723.X

(-) Compounds

Molecule 1 - BASIC ENDOCHITINASE C
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: ORIGAMI(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RSCC
    Organism Common: RYE
    Organism Scientific: SECALE CEREALE
    Organism Taxid: 4550
    Synonym: FAMILY GH 19 CHITINASE, RYE SEED CHITINASE-C, RSC-C

 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  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO43Ligand/IonSULFATE ION
4ZN5Ligand/IonZINC ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:72 , NAG A:302 , HOH A:511 , HOH A:621 , HOH A:650BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARETHR A:69 , GLY A:70 , GLY A:71 , PHE A:86 , NAG A:301 , NAG A:303 , HOH A:472 , HOH A:571BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWARETHR A:68 , THR A:69 , PHE A:86 , ARG A:90 , NAG A:302 , NAG A:304 , HOH A:488 , HOH A:616 , HOH A:645BINDING SITE FOR RESIDUE NAG A 303
04AC4SOFTWAREGLU A:67 , PHE A:86 , GLN A:88 , GLU A:89 , ARG A:90 , GLN A:118 , NAG A:303 , MES A:305 , HOH A:531 , HOH A:593 , HOH A:605 , HOH A:606BINDING SITE FOR RESIDUE NAG A 304
05AC5SOFTWAREILE A:117 , GLN A:118 , LEU A:119 , SER A:120 , ASN A:124 , NAG A:304 , HOH A:446 , HOH A:467 , HOH A:593 , HOH A:606BINDING SITE FOR RESIDUE MES A 305
06AC6SOFTWAREHIS A:8 , ASP A:12 , ARG A:18 , TYR A:29 , THR A:30 , TYR A:31 , ZN A:308 , HOH A:410 , HOH A:432 , HOH A:435 , HOH A:497 , ASP B:51 , HOH B:437BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWARESER A:100 , GLN A:102 , TRP A:103 , SER B:100 , GLN B:102 , TRP B:103BINDING SITE FOR RESIDUE SO4 A 307
08AC8SOFTWAREHIS A:8 , ASP A:12 , SO4 A:306 , ASP B:51BINDING SITE FOR RESIDUE ZN A 308
09AC9SOFTWAREHIS A:17 , ASP A:20 , HOH A:600 , ASP B:232BINDING SITE FOR RESIDUE ZN A 309
10BC1SOFTWAREHIS A:121 , HOH A:506 , HOH A:516 , HOH A:598 , HIS B:206BINDING SITE FOR RESIDUE ZN A 310
11BC2SOFTWAREHIS A:206 , HOH A:492 , HOH A:541 , HOH A:581 , HIS B:121BINDING SITE FOR RESIDUE ZN A 311
12BC3SOFTWARETRP B:72 , NAG B:302BINDING SITE FOR RESIDUE NAG B 301
13BC4SOFTWARETHR B:69 , GLY B:70 , GLY B:71 , CYS B:85 , PHE B:86 , ARG B:90 , NAG B:301 , NAG B:303 , HOH B:448 , HOH B:578BINDING SITE FOR RESIDUE NAG B 302
14BC5SOFTWARETHR B:68 , THR B:69 , PHE B:86 , ARG B:90 , NAG B:302 , NAG B:304 , HOH B:458 , HOH B:496BINDING SITE FOR RESIDUE NAG B 303
15BC6SOFTWAREGLU B:67 , PHE B:86 , GLN B:88 , GLU B:89 , ARG B:90 , GLN B:118 , NAG B:303 , MES B:305 , HOH B:652BINDING SITE FOR RESIDUE NAG B 304
16BC7SOFTWAREILE B:117 , GLN B:118 , LEU B:119 , SER B:120 , ASN B:124 , ILE B:198 , NAG B:304 , HOH B:425 , HOH B:481 , HOH B:487BINDING SITE FOR RESIDUE MES B 305
17BC8SOFTWAREHIS B:8 , ASP B:12 , ARG B:18 , THR B:30 , TYR B:31 , ZN B:307 , HOH B:459 , HOH B:463BINDING SITE FOR RESIDUE SO4 B 306
18BC9SOFTWAREHIS B:8 , ASP B:12 , SO4 B:306 , HOH B:618BINDING SITE FOR RESIDUE ZN B 307

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:23 -A:85
2A:97 -A:105
3A:204 -A:236
4B:23 -B:85
5B:97 -B:105
6B:204 -B:236

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:163 -Pro A:164
2Ala B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_19_1PS00773 Chitinases family 19 signature 1.CHIC_SECCE46-68
 		  2A:23-45
B:23-45
2CHITINASE_19_2PS00774 Chitinases family 19 signature 2.CHIC_SECCE172-182
 		  2A:149-159
B:149-159
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_19_1PS00773 Chitinases family 19 signature 1.CHIC_SECCE46-68
 		  1A:23-45
-
2CHITINASE_19_2PS00774 Chitinases family 19 signature 2.CHIC_SECCE172-182
 		  1A:149-159
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_19_1PS00773 Chitinases family 19 signature 1.CHIC_SECCE46-68
 		  1-
B:23-45
2CHITINASE_19_2PS00774 Chitinases family 19 signature 2.CHIC_SECCE172-182
 		  1-
B:149-159

(-) Exons   (0, 0)

(no "Exon" information available for 4DYG)

(-) 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:242
 aligned with CHIC_SECCE | Q9FRV0 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:242
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
           CHIC_SECCE    24 SVSSIISHAQFDRMLLHRNDGACQAKGFYTYDAFVAAANAFPGFGATGSTDARKRDVAAFLAQTSHETTGGWATAPDGAFAWGYCFKQERGAAADYCTPSAQWPCAPGKRYYGRGPIQLSHNYNYGPAGRAIGVDLLRNPDLVATDPTVSFKTALWFWMTAQAPKPSSHAVITGKWSPSGADRAAGRAPGFGVITNIINGGLECGHGQDSRVADRIGFYKRYCDILGVGYGDNLDCYNQRPF 265
               SCOP domains d4dyga_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1----------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyg A   1 SVSSIISHAQFDRMLLHRNDGACQAKGFYTYDAFVAAANAFPGFGATGSTDARKRDVAAFLAQTSHETTGGWATAPDGAFAWGYCFKQERGAAADYCTPSAQWPCAPGKRYYGRGPIQLSHNYNYGPAGRAIGVDLLRNPDLVATDPTVSFKTALWFWMTAQAPKPSSHAVITGKWSPSGADRAAGRAPGFGVITNIINGGLECGHGQDSRVADRIGFYKRYCDILGVGYGDNLDCYNQRPF 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with CHIC_SECCE | Q9FRV0 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:242
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
           CHIC_SECCE    24 SVSSIISHAQFDRMLLHRNDGACQAKGFYTYDAFVAAANAFPGFGATGSTDARKRDVAAFLAQTSHETTGGWATAPDGAFAWGYCFKQERGAAADYCTPSAQWPCAPGKRYYGRGPIQLSHNYNYGPAGRAIGVDLLRNPDLVATDPTVSFKTALWFWMTAQAPKPSSHAVITGKWSPSGADRAAGRAPGFGVITNIINGGLECGHGQDSRVADRIGFYKRYCDILGVGYGDNLDCYNQRPF 265
               SCOP domains d4dygb_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhh..............hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1----------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyg B   1 SVSSIISHAQFDRMLLHRNDGACQAKGFYTYDAFVAAANAFPGFGATGSTDARKRDVAAFLAQTSHETTGGWATAPDGAFAWGYCFKQERGAAADYCTPSAQWPCAPGKRYYGRGPIQLSHNYNYGPAGRAIGVDLLRNPDLVATDPTVSFKTALWFWMTAQAPKPSSHAVITGKWSPSGADRAAGRAPGFGVITNIINGGLECGHGQDSRVADRIGFYKRYCDILGVGYGDNLDCYNQRPF 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CHIC_SECCE | Q9FRV0)
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.
    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.
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.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    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.
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/Swiss-Prot
        CHIC_SECCE | Q9FRV0: 4dwx 4j0l

(-) Related Entries Specified in the PDB File

4dwx CRYSTAL STRUCTURE OF A FAMILY GH-19 CHITINASE FROM RYE SEEDS