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(-) Description

Title :  NATURAL PRODUCT-GUIDED DISCOVERY OF A FUNGAL CHITINASE INHIBITOR
 
Authors :  C. L. Rush, A. W. Schuttelkopf, R. Hurtadoguerrero, D. E. Blair, A. F. M. S. Desvergnes, I. M. Eggleston, D. M. F. Vanaalten
Date :  18 Oct 10  (Deposition) - 27 Oct 10  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Aspergillosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. L. Rush, A. W. Schuttelkopf, R. Hurtado-Guerrero, D. E. Blair, A. F. M. Ibrahim, S. Desvergnes, I. M. Eggleston, D. M. F. Van Aalten
Natural Product-Guided Discovery Of A Fungal Chitinase Inhibitor.
Chem. Biol. V. 17 1275 2010
PubMed-ID: 21168763  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.07.018

(-) Compounds

Molecule 1 - CHITINASE
    ChainsA, B, C
    EC Number3.2.1.14
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentRESIDUES 29-337
    Organism ScientificASPERGILLUS FUMIGATUS
    Organism Taxid5085
    SynonymCHITINASE A1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PO44Ligand/IonPHOSPHATE ION
3XRG5Ligand/Ion1-METHYL-3-(N-METHYLCARBAMIMIDOYL)UREA
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PO41Ligand/IonPHOSPHATE ION
3XRG2Ligand/Ion1-METHYL-3-(N-METHYLCARBAMIMIDOYL)UREA
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PO42Ligand/IonPHOSPHATE ION
3XRG2Ligand/Ion1-METHYL-3-(N-METHYLCARBAMIMIDOYL)UREA
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PO41Ligand/IonPHOSPHATE ION
3XRG1Ligand/Ion1-METHYL-3-(N-METHYLCARBAMIMIDOYL)UREA

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:34 , ASP A:172 , GLU A:174 , GLN A:230 , TYR A:232 , TRP A:312 , XRG A:1339BINDING SITE FOR RESIDUE XRG A1338
02AC2SOFTWAREGLN A:37 , PHE A:60 , ASN A:76 , ALA A:124 , TYR A:125 , TRP A:312 , XRG A:1338BINDING SITE FOR RESIDUE XRG A1339
03AC3SOFTWARETYR B:34 , ASP B:172 , GLU B:174 , GLN B:230 , TYR B:232 , TRP B:312 , XRG B:1339BINDING SITE FOR RESIDUE XRG B1338
04AC4SOFTWAREGLN B:37 , PHE B:60 , ALA B:124 , TYR B:125 , TRP B:312 , XRG B:1338 , PO4 B:1341BINDING SITE FOR RESIDUE XRG B1339
05AC5SOFTWARETYR C:34 , ALA C:124 , ASP C:172 , GLU C:174 , GLN C:230 , TYR C:232 , TRP C:312BINDING SITE FOR RESIDUE XRG C1337
06AC6SOFTWARETYR A:302 , PRO A:303 , ASP A:304 , THR A:305BINDING SITE FOR RESIDUE PO4 A1340
07AC7SOFTWARETYR C:302 , PRO C:303 , ASP C:304 , THR C:305BINDING SITE FOR RESIDUE PO4 C1338
08AC8SOFTWAREGLN B:80 , CYS B:81 , ASP B:82 , HIS B:101 , GLN B:102BINDING SITE FOR RESIDUE PO4 B1340
09AC9SOFTWAREGLN B:37 , ASN B:76 , GLY B:78 , XRG B:1339BINDING SITE FOR RESIDUE PO4 B1341
10BC1SOFTWAREASP B:304 , THR B:305BINDING SITE FOR RESIDUE CL B1342
11BC2SOFTWAREARG A:43BINDING SITE FOR RESIDUE CL A1341

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:48 -A:110
2A:81 -A:100
3A:208 -A:237
4B:48 -B:110
5B:81 -B:100
6B:208 -B:237
7C:48 -C:110
8C:81 -C:100
9C:208 -C:237

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Gly A:59 -Phe A:60
2Tyr A:125 -Pro A:126
3Ile A:210 -Pro A:211
4Trp A:312 -Glu A:313
5Gly B:59 -Phe B:60
6Tyr B:125 -Pro B:126
7Ile B:210 -Pro B:211
8Trp B:312 -Glu B:313
9Gly C:59 -Phe C:60
10Tyr C:125 -Pro C:126
11Asp C:135 -Ser C:136
12Tyr C:191 -Phe C:192
13Ile C:210 -Pro C:211
14Trp C:312 -Glu C:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA1_ASPFM166-174
 
 
  3A:166-174
B:166-174
C:166-174
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA1_ASPFM166-174
 
 
  1A:166-174
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA1_ASPFM166-174
 
 
  1-
B:166-174
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA1_ASPFM166-174
 
 
  1-
-
C:166-174

(-) Exons   (0, 0)

(no "Exon" information available for 2XUC)

(-) 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:310
 aligned with CHIA1_ASPFM | Q873Y0 from UniProtKB/Swiss-Prot  Length:825

    Alignment length:310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
          CHIA1_ASPFM    28 RSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGNQCDGSVYVTNDGVVTKLLSGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGPVAEGWEGPRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFNQVPERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDTSLGTFNFDAWVTVLKASASKDAKLYVGLPASETAANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILLH 337
               SCOP domains d2xuca_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh.....eeeeeee..hhhhhhhhh....hhhhh...eee.....eeeee..hhhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhh..................eeeeee......hhhhhhhhhhhhhhh......eeee..........hhhhhhhh...eeeee...hhhhhhhhhh.......hhhhhhhhhhh......eeeeeee.hhhhh......hhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhee..eehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xuc A  28 FSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGNQCDGSVYVTNDGVVTKLLSGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGPVAEGWEGPRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFNQVPERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDTSLGTFNFDAWVTVLKASASKDAKLYVGLPASETAANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILLH 337
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with CHIA1_ASPFM | Q873Y0 from UniProtKB/Swiss-Prot  Length:825

    Alignment length:310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
          CHIA1_ASPFM    28 RSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGNQCDGSVYVTNDGVVTKLLSGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGPVAEGWEGPRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFNQVPERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDTSLGTFNFDAWVTVLKASASKDAKLYVGLPASETAANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILLH 337
               SCOP domains d2xucb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh.....eeeeeee..hhhhhhhhh....hhhhh...eee.....eeeee..hhhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhh..................eeeeee......hhhhhhhhhhhhhh.......eeee..........hhhhhhhh...eeeee........hhhhhh......hhhhhhhhhhhh.....eeeeeee.hhhhh......hhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhee..eehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xuc B  28 FSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGNQCDGSVYVTNDGVVTKLLSGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGPVAEGWEGPRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFNQVPERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDTSLGTFNFDAWVTVLKASASKDAKLYVGLPASETAANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILLH 337
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

Chain C from PDB  Type:PROTEIN  Length:293
 aligned with CHIA1_ASPFM | Q873Y0 from UniProtKB/Swiss-Prot  Length:825

    Alignment length:309
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
          CHIA1_ASPFM    28 RSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGNQCDGSVYVTNDGVVTKLLSGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGPVAEGWEGPRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFNQVPERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDTSLGTFNFDAWVTVLKASASKDAKLYVGLPASETAANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILL 336
               SCOP domains d2xucc_ C: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh.....eeeeeee..hhhhhhhhh.......-.-.............--..hhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.-------..........eeeee.......hhhhhhhhhhh...---....eeee..........hhhhhhhh...eeeee.......hhhhhhh.-....hhhhhhhhhhhh.....eeeeeee....-.......hhhhhhhhhhhhhhh....eeeeeee.hhhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xuc C  28 FSNLAIYWGQGPNQLRLSHFCQETSLDIINIGFINYFPDMSPGHWPGSNFGN-C-GSVYVTNDGVVTK--SGCHQIMEDIPICQAAGKKVLLSIGGAYPPDQSILSEDSAVAFATFLWGAFGP-------PRPFGDVVVDGFDFDIEHNGGFGYATMVNTFRQYFN---ERKFYLSAAPQCIIPDAQLSDAIFNAAFDFIWIQYYNTAACSAKSFIDT-LGTFNFDAWVTVLKASASKDAKLYVGLPASET-ANQGYYLTPDEVESLVSTYMDRYPDTFGGIMLWEATASENNQIDGAPYADHMKDILL 336
                                    37        47        57        67        77 | | |  87       | -|      107       117       127       137       147  |      -|      167       177       187     | 197       207       217       227       237       247       257       267       277| |    287       297       307       317       327         
                                                                              79 | |          95 98                                                 150     158                                193 197                                             245 |                            278 |                                                        
                                                                                81 |                                                                                                                                                                 247                              280                                                        
                                                                                  83                                                                                                                                                                                                                                                             

   Legend:   → Mismatch (orange background)
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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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XUC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XUC)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CHIA1_ASPFM | Q873Y0)
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.
    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: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: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:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHIA1_ASPFM | Q873Y02xvn

(-) Related Entries Specified in the PDB File

2xvn A. FUMIGATUS CHITINASE A1 PHENYL-METHYLGUANYLUREA COMPLEX
2xvp CHIA1 FROM ASPERGILLUS FUMIGATUS, APOSTRUCTURE