1CZF - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER

Authors :   Y. Van Santen, K. H. Kalk, B. W. Dijkstra

Date :   02 Sep 99 (Deposition) - 28 Oct 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Beta Helix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Van Santen, J. A. Benen, K. H. Schroter, K. H. Kalk, S. Armand, J. Visser, B. W. Dijkstra
1. 68-A Crystal Structure Of Endopolygalacturonase Ii From Aspergillus Niger And Identification Of Active Site Residue By Site-Directed Mutagenesis.
J. Biol. Chem. V. 274 30474 1999
PubMed-ID: 10521427 | Reference-DOI: 10.1074/JBC.274.43.30474

Molecule 1 - POLYGALACTURONASE II
	Chains	:	A, B
	EC Number	:	3.2.1.15
	Organism Scientific	:	ASPERGILLUS NIGER
	Organism Taxid	:	5061
	Secretion	:	EXTRACELLULAR
	Synonym	:	PG-II, PECTINASE, ENDOPOLYGALACTURONASE II
	Variant	:	NW156

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:54 , ASN A:211 , ASN A:240 , HOH A:647 , HOH A:739 , HOH A:856 , HOH A:897 , HOH A:898 , HOH A:899 , HOH A:906 , HOH A:1002	BINDING SITE FOR RESIDUE NAG A 401
2	AC2	SOFTWARE	GLU B:54 , ASN B:211 , LYS B:239 , ASN B:240 , HOH B:610 , HOH B:747 , HOH B:886 , HOH B:929 , HOH B:968	BINDING SITE FOR RESIDUE NAG B 402
3	AC3	SOFTWARE	ASP A:110 , ASP A:308 , ASP A:336 , HOH A:588	BINDING SITE FOR RESIDUE ZN A 501
4	AC4	SOFTWARE	HIS A:223 , HOH A:535 , HOH A:553 , HOH A:572 , HOH A:578 , HOH A:702	BINDING SITE FOR RESIDUE ZN A 502
5	AC5	SOFTWARE	HIS A:96 , HOH A:606 , HOH A:636 , HOH A:674 , ASP B:28	BINDING SITE FOR RESIDUE ZN A 503
6	AC6	SOFTWARE	ASP B:110 , ASP B:308 , ASP B:336 , HOH B:562	BINDING SITE FOR RESIDUE ZN B 504
7	AC7	SOFTWARE	HIS B:223 , HOH B:603 , HOH B:619 , HOH B:635 , HOH B:674 , HOH B:677	BINDING SITE FOR RESIDUE ZN B 505
8	AC8	SOFTWARE	ASP A:28 , HIS B:96 , HOH B:650 , HOH B:687 , HOH B:779	BINDING SITE FOR RESIDUE ZN B 506

Asymmetric Unit

No.	Residues
1	A:30	-	A:45
2	A:203	-	A:219
3	A:329	-	A:334
4	A:353	-	A:362
5	B:30	-	B:45
6	B:203	-	B:219
7	B:329	-	B:334
8	B:353	-	B:362

Asymmetric Unit

No.	Residues
1	Gly A:87	-	Pro A:88
2	Gly A:228	-	Ser A:229
3	Gly B:87	-	Pro B:88
4	Gly B:228	-	Ser B:229

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR2_ASPNG	216-229	2	A:216-229 B:216-229

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR2_ASPNG	216-229	1	A:216-229 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR2_ASPNG	216-229	1	- B:216-229

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR2_ASPNG	216-229	2	A:216-229 B:216-229

(no "Exon" information available for 1CZF)

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:335
 aligned with PGLR2_ASPNG | P26214 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:335
                                    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       347       357     
          PGLR2_ASPNG    28 DSCTFTTAAAAKAGKAKCSTITLNNIEVPAGTTLDLTGLTSGTKVIFEGTTTFQYEEWAGPLISMSGEHITVTGASGHLINCDGARWWDGKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAFSVQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLESVTGSVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC 362
               SCOP domains d1czfa_ A: Polygalacturonase                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1czfA00 A:28-362 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh................................................................hhhhh......................................................hhhhh............................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------POLYGALACTURON------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1czf A  28 DSCTFTTAAAAKAGKAKCSTITLNNIEVPAGTTLDLTGLTSGTKVIFEGTTTFQYEEWAGPLISMSGEHITVTGASGHLINCDGARWWDGKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAFSVQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLESVTGSVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC 362
                                    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       347       357

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with PGLR2_ASPNG | P26214 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:335
                                    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       347       357     
          PGLR2_ASPNG    28 DSCTFTTAAAAKAGKAKCSTITLNNIEVPAGTTLDLTGLTSGTKVIFEGTTTFQYEEWAGPLISMSGEHITVTGASGHLINCDGARWWDGKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAFSVQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLESVTGSVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC 362
               SCOP domains d1czfb_ B: Polygalacturonase                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1czfB00 B:28-362 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhh.eeeee..ee.....eee.......eeeee.eeee.........eeeeee..eeee....eee.hhhhh..............eeeeeee.eeee..eee......eeee.eeeeee..eee.hhhhh........eee...eeeeee..eee.....eee..eeeeeee..eee....eeeeee......eeeeeeeeeeeee...eeeeeeee....eeeeeeeeeeeeeeee..eeeeeeeeee..ee.......eeeeeeeeeeeeeee....eeeeee.....eeeeeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------POLYGALACTURON------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1czf B  28 DSCTFTTAAAAKAGKAKCSTITLNNIEVPAGTTLDLTGLTSGTKVIFEGTTTFQYEEWAGPLISMSGEHITVTGASGHLINCDGARWWDGKGTSGKKKPKFFYAHGLDSSSITGLNIKNTPLMAFSVQANDITFTDVTINNADGDTQGGHNTDAFDVGNSVGVNIIKPWVHNQDDCLAVNSGENIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLESVTGSVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC 362
                                    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       347       357

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Single-stranded right-handed beta-helix (140)

Superfamily: Pectin lyase-like (89)

Family: Galacturonase (11)

Protein domain: Polygalacturonase (9)

Fungus (Aspergillus niger), endo-polygalacturonase II [TaxId: 5061] (1)

1a	d1czfa_	A:
1b	d1czfb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: Pectate Lyase C-like (105)

Homologous Superfamily: Single-stranded right-handed beta-helix, Pectin lyase-like (73)

Aspergillus niger. Organism_taxid: 5061. Variant: nw156. (1)

1a	1czfA00	A:28-362
1b	1czfB00	B:28-362

(no "Pfam Domain" information available for 1CZF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGLR2_ASPNG | P26214)

molecular function
	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:0004650	polygalacturonase activity	Catalysis of the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	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.
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
		Gly A:228 - Ser A:229	[ RasMol ]
		Gly A:87 - Pro A:88	[ RasMol ]
		Gly B:228 - Ser B:229	[ RasMol ]
		Gly B:87 - Pro B:88	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

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