1IDK - JenaLib

Title :   PECTIN LYASE A

Authors :   O. Mayans, M. Scott, I. Connerton, T. Gravesen, J. Benen, J. Visser, R. Pickersgill, J. Jenkins

Date :   04 Oct 96 (Deposition) - 15 Oct 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym./Biol. Unit : A

Keywords :   Lyase, Signal, Glycoprotein, Multigene Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Mayans, M. Scott, I. Connerton, T. Gravesen, J. Benen, J. Visser, R. Pickersgill, J. Jenkins
Two Crystal Structures Of Pectin Lyase A From Aspergillus Reveal A Ph Driven Conformational Change And Striking Divergence In The Substrate-Binding Clefts Of Pectin And Pectate Lyases.
Structure V. 5 677 1997
PubMed-ID: 9195887 | Reference-DOI: 10.1016/S0969-2126(97)00222-0
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (1, 1)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

Asymmetric/Biological Unit (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PELA_ASPNG_001 *	E	32	K	PELA_ASPNG	---	---	A	K	12	K
2	UniProt	VAR_PELA_ASPNG_002 *	D	39	S	PELA_ASPNG	---	---	A	S	19	S
3	UniProt	VAR_PELA_ASPNG_003 *	V	121	T	PELA_ASPNG	---	---	A	T	101	T
4	UniProt	VAR_PELA_ASPNG_004 *	G	233	A	PELA_ASPNG	---	---	A	A	213	A
5	UniProt	VAR_PELA_ASPNG_005 *	C	268	A	PELA_ASPNG	---	---	A	A	248	A
6	UniProt	VAR_PELA_ASPNG_006 *	F	273	W	PELA_ASPNG	---	---	A	W	253	W
7	UniProt	VAR_PELA_ASPNG_007 *	A	309	E	PELA_ASPNG	---	---	A	E	289	E
8	UniProt	VAR_PELA_ASPNG_008 *	T	316	S	PELA_ASPNG	---	---	A	S	296	S
9	UniProt	VAR_PELA_ASPNG_009 *	C	337	S	PELA_ASPNG	---	---	A	S	317	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:359
 aligned with PELA_ASPNG | Q01172 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:359
                                    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       340       350       360       370         
           PELA_ASPNG    21 VGVSGSAEGFAEGVTGGGDATPVYPDTIDELVSYLGDDEARVIVLTKTFDFTDSEGTTTGTGCAPWGTASACQVAIDQDDWCENYEPDAPSVSVEYYNAGVLGITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINPKYVWGGDAITLDDCDLVWIDHVTTARIGRQHYVLGTSADNRVSLTNNYIDGVSDYSATCDGYHYWGIYLDGDADLVTMKGNYIYHTSGRSPKVQDNTLLHCVNNYFYDISGHAFEIGEGGYVLAEGNVFQNVDTVLETYEGAAFTVPSTTAGEVCSTYLGRDCVINGFGCSGTFSEDSTSFLSDFEGKNIASASAYTSVASRVVANAGQGNL 379
               SCOP domains d1idka_ A: Pectin lyase                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1idkA00 A:1-359 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhh....eeeee..eee......eeeeeee..............hhhhhhh......eeeeeee......eee...eeeee.....eee...eee......eeee..eee............eee.....eeee..eee......eee......eeeee..eee................eee.....eeeee..eee.............eeeee..eee......eee....eeeee..eee.....eeee..eee....hhhhhhhhhhh.......eee............hhhh..........hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------K------S---------------------------------------------------------------------------------T---------------------------------------------------------------------------------------------------------------A----------------------------------A----W-----------------------------------E------S--------------------S------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1idk A   1 VGVSGSAEGFAKGVTGGGSATPVYPDTIDELVSYLGDDEARVIVLTKTFDFTDSEGTTTGTGCAPWGTASACQVAIDQDDWCENYEPDAPSVSVEYYNAGTLGITVTSNKSLIGEGSSGAIKGKGLRIVSGAENIIIQNIAVTDINPKYVWGGDAITLDDCDLVWIDHVTTARIGRQHYVLGTSADNRVSLTNNYIDGVSDYSATCDGYHYWAIYLDGDADLVTMKGNYIYHTSGRSPKVQDNTLLHAVNNYWYDISGHAFEIGEGGYVLAEGNVFQNVDTVLETYEGEAFTVPSSTAGEVCSTYLGRDCVINGFGSSGTFSEDSTSFLSDFEGKNIASASAYTSVASRVVANAGQGNL 359
                                    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       340       350

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PELA_ASPNG | Q01172)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0047490	pectin lyase activity	Catalysis of the reaction: a pectin = an oligosaccharide with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronate end + a pectin. This reaction is the eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their nonreducing ends.
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: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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