2IUZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH C2-DICAFFEINE

Authors :   A. W. Schuttelkopf, O. A. Andersen, F. V. Rao, M. Allwood, C. M. Lloyd, I. M. Eggleston, D. M. F. Van Aalten

Date :   08 Jun 06 (Deposition) - 12 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Glycosidase, (Beta-Alpha)8 Barrel, Chitinase- C2Dicaffeine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. W. Schuttelkopf, O. A. Andersen, F. V. Rao, M. Allwood, C. M. Lloyd, I. M. Eggleston, D. M. F. Van Aalten
Screening-Based Discovery And Structural Dissection Of A Novel Family 18 Chitinase Inhibitor
J. Biol. Chem. V. 281 27278 2006
PubMed-ID: 16844689 | Reference-DOI: 10.1074/JBC.M604048200

Molecule 1 - CHITINASE
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLYSS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PGEX-6P-1
	Fragment	:	RESIDUES 1-433
	Organism Scientific	:	ASPERGILLUS FUMIGATUS
	Organism Taxid	:	5085
	Synonym	:	ASPERGILLUS FUMIGATUS CHITINASE B1, CLASS V CHITINASE CHIB1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	D1H	2	Ligand/Ion	1,1'-ETHANE-1,2-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE)
2	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	D1H	1	Ligand/Ion	1,1'-ETHANE-1,2-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE)
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	D1H	1	Ligand/Ion	1,1'-ETHANE-1,2-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE)
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:126 , GLN A:414 , HOH A:2442 , SER B:103	BINDING SITE FOR RESIDUE SO4 A1434
02	AC2	SOFTWARE	THR A:149 , ASP A:150 , HOH A:2168 , HOH A:2457	BINDING SITE FOR RESIDUE SO4 A1435
03	AC3	SOFTWARE	ASN A:181 , ASP A:182 , HOH A:2458	BINDING SITE FOR RESIDUE SO4 A1436
04	AC4	SOFTWARE	HIS A:229 , LEU A:230 , LYS A:231 , ASP A:232 , HOH A:2247 , HOH A:2459 , HOH A:2460	BINDING SITE FOR RESIDUE SO4 A1437
05	AC5	SOFTWARE	ASN A:354 , HOH A:2461 , HOH A:2462	BINDING SITE FOR RESIDUE SO4 A1438
06	AC6	SOFTWARE	LEU A:341 , TYR A:348 , HOH A:2369 , HOH A:2463 , HOH A:2464 , PRO B:81 , HOH B:2137	BINDING SITE FOR RESIDUE SO4 A1439
07	AC7	SOFTWARE	THR B:149 , ASP B:150 , HOH B:2403 , HOH B:2404	BINDING SITE FOR RESIDUE SO4 B1433
08	AC8	SOFTWARE	ASN A:323 , GLU B:338 , HIS B:339 , HOH B:2406 , HOH B:2407 , HOH B:2408	BINDING SITE FOR RESIDUE SO4 B1434
09	AC9	SOFTWARE	ASN B:181 , ASP B:182	BINDING SITE FOR RESIDUE SO4 B1435
10	BC1	SOFTWARE	ARG B:283 , ALA B:289 , HOH B:2263 , HOH B:2409 , HOH B:2410	BINDING SITE FOR RESIDUE SO4 B1436
11	BC2	SOFTWARE	HIS B:229 , LEU B:230 , LYS B:231 , ASP B:232 , HOH B:2411 , HOH B:2412	BINDING SITE FOR RESIDUE SO4 B1437
12	BC3	SOFTWARE	TRP A:52 , PHE A:76 , GLY A:136 , TRP A:137 , THR A:138 , TYR A:139 , ASP A:246 , TYR A:299 , TRP A:384 , HOH A:2262 , HOH A:2465 , HOH A:2466	BINDING SITE FOR RESIDUE D1H A1440
13	BC4	SOFTWARE	GLN A:364 , TRP B:52 , PHE B:76 , GLY B:136 , TRP B:137 , THR B:138 , TYR B:245 , ASP B:246 , TYR B:299 , TRP B:384 , HOH B:2005 , HOH B:2126 , HOH B:2221 , HOH B:2291 , HOH B:2413 , HOH B:2415	BINDING SITE FOR RESIDUE D1H B1438

(no "SS Bond" information available for 2IUZ)

Asymmetric Unit

No.	Residues
1	Ala A:75	-	Phe A:76
2	Glu A:177	-	Tyr A:178
3	Leu A:331	-	Pro A:332
4	Trp A:384	-	Asp A:385
5	Ala B:75	-	Phe B:76
6	Glu B:177	-	Tyr B:178
7	Leu B:331	-	Pro B:332
8	Trp B:384	-	Asp B:385

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	2	A:169-177 B:169-177

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	1	A:169-177 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	1	- B:169-177

(no "Exon" information available for 2IUZ)

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:395
 aligned with CHIB1_ASPFM | Q873X9 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:395
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
          CHIB1_ASPFM    39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT 433
               SCOP domains d2iuza1 A:39-298,A:361-433 Chitinase 1                                                                                                                                                                                                                              d2iuza2 A:299-360 Chitinase 1                                 d2iuza1 A:39-298,A:361-433 Chitinase 1                                    SCOP domains
               CATH domains 2iuzA01 A:39-297,A:361-433 Glycosidases                                                                                                                                                                                                                            2iuzA02 A:298-360  [code=3.10.50.10, no name defined]          2iuzA01 A:39-297,A:361-433 Glycosidases                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee..........hhhhhhh...............hhhhhhhhhhhhhh...eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhh.eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhh.hhhh..............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iuz A  39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT 433
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with CHIB1_ASPFM | Q873X9 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:395
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
          CHIB1_ASPFM    39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT 433
               SCOP domains d2iuzb1 B:39-298,B:361-433 Chitinase 1                                                                                                                                                                                                                              d2iuzb2 B:299-360 Chitinase 1                                 d2iuzb1 B:39-298,B:361-433 Chitinase 1                                    SCOP domains
               CATH domains 2iuzB01 B:39-297,B:361-433 Glycosidases                                                                                                                                                                                                                            2iuzB02 B:298-360  [code=3.10.50.10, no name defined]          2iuzB01 B:39-297,B:361-433 Glycosidases                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee..........hhhhhh................hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhh.eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iuz B  39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT 433
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: FKBP-like (309)

Superfamily: Chitinase insertion domain (107)

Family: Chitinase insertion domain (107)

Protein domain: Chitinase 1 (18)

Aspergillus fumigatus [TaxId: 5085] (14)

1a	d2iuza2	A:299-360
1b	d2iuzb2	B:299-360

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: Type II chitinase (131)

Protein domain: Chitinase 1 (18)

Aspergillus fumigatus [TaxId: 5085] (14)

2a	d2iuza1	A:39-298,A:361-433
2b	d2iuzb1	B:39-298,B:361-433

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Aspergillus fumigatus. Organism_taxid: 5085. (5)

1a	2iuzA01	A:39-297,A:361-433
1b	2iuzB01	B:39-297,B:361-433

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.10, no name defined] (121)

Aspergillus fumigatus. Organism_taxid: 5085. (5)

2a	2iuzA02	A:298-360
2b	2iuzB02	B:298-360

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHIB1_ASPFM | Q873X9)

molecular function
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:75 - Phe A:76	[ RasMol ]
		Ala B:75 - Phe B:76	[ RasMol ]
		Glu A:177 - Tyr A:178	[ RasMol ]
		Glu B:177 - Tyr B:178	[ RasMol ]
		Leu A:331 - Pro A:332	[ RasMol ]
		Leu B:331 - Pro B:332	[ RasMol ]
		Trp A:384 - Asp A:385	[ RasMol ]
		Trp B:384 - Asp B:385	[ RasMol ]

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	2iuz
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	CHIB1_ASPFM \| Q873X9	:	1w9p 1w9u 1w9v 1wno 2a3a 2a3b 2a3c 2a3e 3ch9 3chc 3chd 3che 3chf

1w9p	SPECIFICITY AND AFFINITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITORS AGAINST ASPERGILLUS FUMIGATUS, HUMAN AND BACTERIAL CHITINASEFRA
1w9u	SPECIFICITY AND AFFNITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITOR ARGADIN AGAINST ASPERGILLUS FUMIGATUS CHITINASE
1w9v	SPECIFICITY AND AFFINITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE ARGIFIN AGAINST ASPERGILLUS FUMIGATUS
2a3a	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 INCOMPLEX WITH THEOPHYLLINE
2a3b	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 INCOMPLEX WITH CAFFEINE
2a3c	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 INCOMPLEX WITH PENTOXIFYLLINE
2a3e	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 INCOMPLEX WITH ALLOSAMIDIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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