2XHN - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   RHAMNOGALACTURONAN LYASE FROM ASPERGILLUS ACULEATUS K150A ACTIVE SITE MUTANT

Authors :   M. H. Jensen, H. Otten, U. Christensen, T. V. Borchert, L. L. H. Christen S. Larsen, L. Lo Leggio

Date :   18 Jun 10 (Deposition) - 29 Sep 10 (Release) - 20 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.52

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

Keywords :   Carbohydrate Active Enzyme, Lyase, Pectin, Degradation, Polysaccharide Lyase Family 4 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Jensen, H. Otten, U. Christensen, T. V. Borchert, L. L. H. Christensen, S. Larsen, L. L. Leggio
Structural And Biochemical Studies Elucidate The Mechanism Of Rhamnogalacturonan Lyase From Aspergillus Aculeatus.
J. Mol. Biol. V. 404 100 2010
PubMed-ID: 20851126 | Reference-DOI: 10.1016/J.JMB.2010.09.013

Molecule 1 - RHAMNOGALACTURONASE B
	Chains	:	A, B
	EC Number	:	4.2.2.10
	Engineered	:	YES
	Expression System	:	ASPERGILLUS ORYZAE
	Expression System Taxid	:	5062
	Mutation	:	YES
	Organism Scientific	:	ASPERGILLUS ACULEATUS
	Organism Taxid	:	5053
	Synonym	:	RHAMNOGALACTURONAN LYASE, RGASE B, RHG B

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:347 , ASP A:349 , GLN A:351 , ASP A:502 , HOH A:2761	BINDING SITE FOR RESIDUE CA A 800
02	AC2	SOFTWARE	ASN A:19 , SER A:229 , ARG A:230 , SER A:231 , GLY A:232 , HOH A:2067 , HOH A:2571 , HOH A:2941 , HOH A:2942 , HOH A:2943 , HOH A:2945	BINDING SITE FOR RESIDUE SO4 A 901
03	AC3	SOFTWARE	LYS A:395 , SER A:490 , HOH A:2946 , HOH A:2947 , HOH A:2948	BINDING SITE FOR RESIDUE SO4 A 902
04	AC4	SOFTWARE	ARG A:429 , GLY A:488 , HOH A:2949 , HOH A:2951 , HOH A:2952	BINDING SITE FOR RESIDUE SO4 A 903
05	AC5	SOFTWARE	SER A:53 , ARG A:107 , ARG A:111 , HOH A:2537 , HOH A:2954	BINDING SITE FOR RESIDUE SO4 A 904
06	AC6	SOFTWARE	SER A:369 , HOH A:2775 , HOH A:2777 , HOH A:2955 , HOH A:2956	BINDING SITE FOR RESIDUE EDO A1509
07	AC7	SOFTWARE	GLU B:347 , ASP B:349 , GLN B:351 , ASP B:502 , HOH B:2725	BINDING SITE FOR RESIDUE CA B 801
08	AC8	SOFTWARE	ASN B:19 , SER B:229 , ARG B:230 , SER B:231 , GLY B:232 , HOH B:2059 , HOH B:2528 , HOH B:2534 , HOH B:2920 , HOH B:2922	BINDING SITE FOR RESIDUE SO4 B 905
09	AC9	SOFTWARE	LYS B:395 , SER B:490 , HOH B:2780 , HOH B:2781	BINDING SITE FOR RESIDUE SO4 B 906
10	ACA	AUTHOR	ALA A:150 , HIS A:210	ACTIVE SITE
11	ACB	AUTHOR	ALA B:150 , HIS B:210	ACTIVE SITE
12	BC1	SOFTWARE	ARG B:429 , GLY B:488 , HOH B:2923	BINDING SITE FOR RESIDUE SO4 B 907
13	BC2	SOFTWARE	GLN B:47 , SER B:53 , ARG B:107 , ARG B:111 , HOH B:2496 , HOH B:2926 , HOH B:2927	BINDING SITE FOR RESIDUE SO4 B 908

Asymmetric Unit

No.	Residues
1	A:30	-	A:73
2	A:164	-	A:173
3	B:30	-	B:73
4	B:164	-	B:173

Asymmetric Unit

No.	Residues
1	Glu A:121	-	Pro A:122
2	Gly A:222	-	Pro A:223
3	Gly A:375	-	Pro A:376
4	Asn A:399	-	Pro A:400
5	Glu B:121	-	Pro B:122
6	Gly B:222	-	Pro B:223
7	Gly B:375	-	Pro B:376
8	Asn B:399	-	Pro B:400

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

(no "PROSITE Motif" information available for 2XHN)

(no "Exon" information available for 2XHN)

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:508
 aligned with RGLA_ASPAC | Q00019 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:508
                                    29        39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        
           RGLA_ASPAC    20 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSKFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 527
               SCOP domains d2xhna1 A:1-250 automated matches                                                                                                                                                                                                                         d2xhna2 A:251-337 automated matches                                                    d2xhna3 A:338-508 automated matches                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeee......eeeeee.....eeeeee..ee........ee.......eeeeeee..eeeeeee...eeeeeeee....eeeeeeee........eeeeeee......eee.hhhhhh....eeee...eeee..eeehhhhhh..hhhh.eeeee....eeeee.................eee....eeeeeeee...........eeeeeeeeeee..........hhhhhhh......hhhhh.eeeeeee.......eeeeee....eeeee.....eee......eeeeeeeee..eeeeeeeeee....eee..ee......eeeeeee..........hhhhhh...............eee....hhhhh..eee......eeeeeeehhhhh..eeeeeeeeeee...eeeeee..ee.............hhhhh.......eeeeee.......eeeeeeeeee.....hhhhh.eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhn A   1 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSAFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 508
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500

Chain B from PDB  Type:PROTEIN  Length:508
 aligned with RGLA_ASPAC | Q00019 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:508
                                    29        39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        
           RGLA_ASPAC    20 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSKFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 527
               SCOP domains d2xhnb1 B:1-250 automated matches                                                                                                                                                                                                                         d2xhnb2 B:251-337 automated matches                                                    d2xhnb3 B:338-508 automated matches                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeee......eeeeee.....eeeeee..ee........ee.......eeeeeee..eeeeeee...eeeeeeee....eeeeeeee........eeeeeee......eee.hhhhhh....eeee...eeee..eeehhhhhh..hhhh.eeeee....eeeee.................eee....eeeeeeee...........eeeeeeeeeee..........hhhhhhh......hhhhh.eeeeeee.......eeeeee....eeeee.....eee......eeeeeeeee..eeeeeeeeee....eee..ee.......eeeeee..........hhhhhh...............eee....hhhhh..eee......eeeeeeehhhhh..eeeeeeeeeee...eeeeee..ee.............hhhhh.......eeeeee.......eeeeeeeeee.....hhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhn B   1 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSAFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 508
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500

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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (RGLA_ASPAC | Q00019)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016837	carbon-oxygen lyase activity, acting on polysaccharides	Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0102210	rhamnogalacturonan endolyase activity	Catalysis of the reaction: H2O + a rhamnogalacturonan type I <=> [rhamnogalacturonan I oligosaccharide]-alpha-L-rhamnose + 4-deoxy-4,5-unsaturated D-galactopyranosyluronate-[rhamnogalacturonan I oligosaccharide]
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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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	Cis Peptide Bonds
		Asn A:399 - Pro A:400	[ RasMol ]
		Asn B:399 - Pro B:400	[ RasMol ]
		Glu A:121 - Pro A:122	[ RasMol ]
		Glu B:121 - Pro B:122	[ RasMol ]
		Gly A:222 - Pro A:223	[ RasMol ]
		Gly A:375 - Pro A:376	[ RasMol ]
		Gly B:222 - Pro B:223	[ RasMol ]
		Gly B:375 - Pro B:376	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2xhn
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	RGLA_ASPAC \| Q00019
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	4.2.2.10
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	RGLA_ASPAC \| Q00019
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UniProtKB/Swiss-Prot
	RGLA_ASPAC \| Q00019	:	1nkg 3njv 3njx

1nkg	RHAMNOGALACTURONAN LYASE FROM ASPERGILLUS ACULEATUS
3njv	RHAMNOGALACTURONAN LYASE FROM ASPERGILLUS ACULEATUS MUTANT K150A SUBSTRATE COMPLEX RELATED ENTRIES
3njx	RHAMNOGALACTURONAN LYASE FROM ASPERGILLUS ACULEATUS MUTANT H210A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (13, 13)

SS Bonds (4, 4)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries

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Related Entries Specified in the PDB File