1IB4 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS AT PH4.5

Authors :   S. W. Cho, W. Shin

Date :   27 Mar 01 (Deposition) - 19 Sep 01 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Polygalacturonase, Glycosylhydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. W. Cho, S. Lee, W. Shin
The X-Ray Structure Of Aspergillus Aculeatus Polygalacturonase And A Modeled Structure Of The Polygalacturonase-Octagalacturonate Complex.
J. Mol. Biol. V. 311 863 2001
PubMed-ID: 11518536 | Reference-DOI: 10.1006/JMBI.2001.4919

Molecule 1 - POLYGALACTURONASE
	Chains	:	A, B
	EC Number	:	3.2.1.15
	Organism Scientific	:	ASPERGILLUS ACULEATUS
	Organism Taxid	:	5053

		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 (3, 29)

No.	Name	Count	Type	Full Name
1	CD	3	Ligand/Ion	CADMIUM ION
2	MAN	22	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 13)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	MAN	11	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 13)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	MAN	11	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:202 , ASP A:231 , GLU B:95	BINDING SITE FOR RESIDUE CD B 935
02	AC2	SOFTWARE	GLU A:95 , HIS B:202 , ASP B:231 , HOH B:1309	BINDING SITE FOR RESIDUE CD B 936
03	AC3	SOFTWARE	ASP B:285 , ASP B:313	BINDING SITE FOR RESIDUE CD B 937
04	AC4	SOFTWARE	THR A:5 , HOH A:1164	BINDING SITE FOR MONO-SACCHARIDE MAN A 405 BOUND TO THR A 5
05	AC5	SOFTWARE	SER A:7 , HOH A:1285 , ARG B:212 , SER B:213 , ASN B:215	BINDING SITE FOR MONO-SACCHARIDE MAN A 407 BOUND TO SER A 7
06	AC6	SOFTWARE	SER A:9 , HOH A:1004 , HOH A:1200 , THR B:165 , THR B:167 , GLU B:189 , ASP B:214	BINDING SITE FOR MONO-SACCHARIDE MAN A 409 BOUND TO SER A 9
07	AC7	SOFTWARE	ASN A:10 , SER A:13 , LYS A:17 , MAN A:414 , MAN A:416	BINDING SITE FOR MONO-SACCHARIDE MAN A 413 BOUND TO SER A 13
08	AC8	SOFTWARE	ASN A:10 , SER A:14 , MAN A:413 , MAN A:418	BINDING SITE FOR MONO-SACCHARIDE MAN A 414 BOUND TO SER A 14
09	AC9	SOFTWARE	SER A:13 , SER A:16 , MAN A:413 , HOH A:1291	BINDING SITE FOR MONO-SACCHARIDE MAN A 416 BOUND TO SER A 16
10	BC1	SOFTWARE	PHE A:6 , SER A:14 , SER A:18 , MAN A:414 , ALA B:1 , THR B:2 , THR B:3	BINDING SITE FOR MONO-SACCHARIDE MAN A 418 BOUND TO SER A 18
11	BC2	SOFTWARE	SER A:21 , CYS A:22 , SER A:23 , ASN A:44 , THR A:47	BINDING SITE FOR MONO-SACCHARIDE MAN A 423 BOUND TO SER A 23
12	BC3	SOFTWARE	THR A:24 , HIS A:48	BINDING SITE FOR MONO-SACCHARIDE MAN A 424 BOUND TO THR A 24
13	BC4	SOFTWARE	SER A:34 , HOH A:1181 , HOH A:1192 , ASP B:136	BINDING SITE FOR MONO-SACCHARIDE MAN A 434 BOUND TO SER A 34
14	BC5	SOFTWARE	TYR A:168 , ASN A:190 , TYR A:192 , ASN A:219 , HOH A:1047 , HOH A:1103 , HOH A:1288	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 219 RESIDUES 351 TO 353
15	BC6	SOFTWARE	THR B:3 , THR B:5 , THR B:243	BINDING SITE FOR MONO-SACCHARIDE MAN B 405 BOUND TO THR B 5
16	BC7	SOFTWARE	SER A:213 , THR B:5 , SER B:7	BINDING SITE FOR MONO-SACCHARIDE MAN B 407 BOUND TO SER B 7
17	BC8	SOFTWARE	GLU A:189 , ASP A:214 , THR A:216 , SER B:9 , ASN B:10 , HOH B:1170	BINDING SITE FOR MONO-SACCHARIDE MAN B 409 BOUND TO SER B 9
18	BC9	SOFTWARE	SER B:13 , LYS B:17 , MAN B:416 , HOH B:1328	BINDING SITE FOR MONO-SACCHARIDE MAN B 413 BOUND TO SER B 13
19	CC1	SOFTWARE	ASN B:10 , SER B:14 , MAN B:418 , HOH B:1104	BINDING SITE FOR MONO-SACCHARIDE MAN B 414 BOUND TO SER B 14
20	CC2	SOFTWARE	SER B:16 , MAN B:413 , HOH B:1054	BINDING SITE FOR MONO-SACCHARIDE MAN B 416 BOUND TO SER B 16
21	CC3	SOFTWARE	ALA A:1 , THR A:2 , THR A:3 , PHE B:6 , LYS B:17 , SER B:18 , MAN B:414	BINDING SITE FOR MONO-SACCHARIDE MAN B 418 BOUND TO SER B 18
22	CC4	SOFTWARE	ALA B:1 , SER B:23 , GLY B:46 , HOH B:1206 , HOH B:1213 , HOH B:1273	BINDING SITE FOR MONO-SACCHARIDE MAN B 423 BOUND TO SER B 23
23	CC5	SOFTWARE	THR B:3 , THR B:24	BINDING SITE FOR MONO-SACCHARIDE MAN B 424 BOUND TO THR B 24
24	CC6	SOFTWARE	SER B:34 , HOH B:1216	BINDING SITE FOR MONO-SACCHARIDE MAN B 434 BOUND TO SER B 34
25	CC7	SOFTWARE	TYR B:168 , ASN B:190 , TYR B:192 , ASN B:219 , HOH B:1087 , HOH B:1194 , HOH B:1260	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 219 RESIDUES 351 TO 353

Asymmetric Unit

No.	Residues
1	A:4	-	A:22
2	A:182	-	A:198
3	A:306	-	A:311
4	A:330	-	A:339
5	B:4	-	B:22
6	B:182	-	B:198
7	B:306	-	B:311
8	B:330	-	B:339

Asymmetric Unit

No.	Residues
1	Gly A:64	-	Pro A:65
2	Gly A:207	-	Ser A:208
3	Gly B:64	-	Pro B:65
4	Gly B:207	-	Ser B:208

(no "SAP(SNP)/Variant" information available for 1IB4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR1_ASPAC	234-247	2	A:195-208 B:195-208

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR1_ASPAC	234-247	1	A:195-208 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYGALACTURONASE	PS00502	Polygalacturonase active site.	PGLR1_ASPAC	234-247	1	- B:195-208

(no "Exon" information available for 1IB4)

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:339
 aligned with PGLR1_ASPAC | O74213 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:339
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369         
          PGLR1_ASPAC    40 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 378
               SCOP domains d1ib4a_ A: Polygalacturonase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ib4A00 A:1-339 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh.eeeeeeeee.....eee.......eeeee.eeee.........eeeeee..eeee....eee.hhhhh...hhhhh.......eeeeeeeeeeee..eee......eeee..eeeeee..eee.hhhh.........eee...eeeeee..eee.....eee..eeeeeee..eee....eeeeee......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeee............eeeeeeeeeeeee....eeeeee.....eeeeeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------POLYGALACTURON----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ib4 A   1 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 339
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with PGLR1_ASPAC | O74213 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:339
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369         
          PGLR1_ASPAC    40 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 378
               SCOP domains d1ib4b_ B: Polygalacturonase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ib4B00 B:1-339 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh.eeeeeeeee.....eee.......eeeee.eeee.........eeeeee..eeee....eee.hhhhh...hhhhh.......eeeeeeeeeeee..eee......eeee..eeeeee..eee.hhhh.........eee...eeeeee..eee.....eee..eeeeeee..eee....eeeeee......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeee............eeeeeeeeeeeee....eeeeee.....eeeeeee..eee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------POLYGALACTURON----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ib4 B   1 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 339
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

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: 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 aculeatus) [TaxId: 5053] (2)

1a	d1ib4a_	A:
1b	d1ib4b_	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 aculeatus. Organism_taxid: 5053 (2)

1a	1ib4A00	A:1-339
1b	1ib4B00	B:1-339

(no "Pfam Domain" information available for 1IB4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGLR1_ASPAC | O74213)

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:207 - Ser A:208	[ RasMol ]
		Gly A:64 - Pro A:65	[ RasMol ]
		Gly B:207 - Ser B:208	[ RasMol ]
		Gly B:64 - Pro B:65	[ RasMol ]

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	1ib4
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	PGLR1_ASPAC \| O74213	:	1ia5

1bhe	1BHE CONTAINS THE SAME PROTEIN FROM ERWINIA CAROTOVORA SSP.CAROTOVORA
1czf	1CZF CONTAINS ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER
1ia5	1IA5 CONTAINS THE SAME PROTEIN AT PH8.5
1rmg	1RMG CONTAINS RHAMNOGALACTURONASE A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 29)

Sites (25, 25)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Related Entries Specified in the PDB File