3B90 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PECTATE LYASE PELI FROM ERWINIA CHRYSANTHEMI

Authors :   C. Creze, S. Castang, E. Derivery, R. Haser, V. Shevchik, P. Gouet

Date :   02 Nov 07 (Deposition) - 29 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: A (1x),B (1x)

Keywords :   Pectate Lyase, Pectin, Galacturonic Acid, Erwinia Chrysanthemi, Right-Handed Parallel Beta Helix Fold, Catalytic Domain, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Creze, S. Castang, E. Derivery, R. Haser, N. Hugouvieux-Cotte-Pattat, V. E. Shevchik, P. Gouet
The Crystal Structure Of Pectate Lyase Peli From Soft Rot Pathogen Erwinia Chrysanthemi In Complex With Its Substrate
J. Biol. Chem. V. 283 18260 2008
PubMed-ID: 18430740 | Reference-DOI: 10.1074/JBC.M709931200

Molecule 1 - ENDO-PECTATE LYASE
	Chains	:	A, B
	EC Number	:	4.2.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-6
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PELI
	Organism Scientific	:	ERWINIA CHRYSANTHEMI
	Organism Taxid	:	556

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:191 , ILE A:192 , ASN A:213 , TYR A:218 , HOH A:1147 , HOH A:1148	BINDING SITE FOR RESIDUE CA A 701
2	AC2	SOFTWARE	ASP B:191 , ILE B:192 , ASN B:213 , TYR B:218	BINDING SITE FOR RESIDUE CA B 702
3	AC3	SOFTWARE	ASP A:173 , GLU A:194 , ASP A:195 , HOH A:1247 , HOH A:1248	BINDING SITE FOR RESIDUE ZN A 711
4	AC4	SOFTWARE	HIS A:176 , ASP A:178 , HOH A:1160	BINDING SITE FOR RESIDUE ZN A 712
5	AC5	SOFTWARE	ASP B:173 , GLU B:194 , ASP B:195 , THR B:198 , HOH B:1249	BINDING SITE FOR RESIDUE ZN B 713
6	AC6	SOFTWARE	ASP A:148 , HIS B:176 , ASP B:178 , HOH B:1263	BINDING SITE FOR RESIDUE ZN B 714
7	AC7	SOFTWARE	LYS B:249 , ARG B:252 , PHE B:312 , LYS B:324 , HOH B:1172 , HOH B:1324	BINDING SITE FOR RESIDUE SO4 B 721
8	AC8	SOFTWARE	THR A:269 , SER A:270 , LYS B:238 , GLY B:239 , THR B:269 , SER B:270 , HOH B:1309	BINDING SITE FOR RESIDUE SO4 A 722

Asymmetric Unit

No.	Residues
1	A:121	-	A:134
2	A:143	-	A:193
3	A:177	-	A:182
4	A:254	-	A:257
5	A:309	-	A:334
6	B:121	-	B:134
7	B:143	-	B:193
8	B:177	-	B:182
9	B:254	-	B:257
10	B:309	-	B:334

Asymmetric Unit

No.	Residues
1	Gly A:262	-	Pro A:263
2	Lys A:305	-	Pro A:306
3	Gly B:262	-	Pro B:263
4	Lys B:305	-	Pro B:306

(no "SAP(SNP)/Variant" information available for 3B90)

(no "PROSITE Motif" information available for 3B90)

(no "Exon" information available for 3B90)

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:226
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:226
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338      
         O50325_DICCH   119 SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eee....ee......hhhhh...eeee..eeeeeee........eeeee.eeeeeeeee.......eee...eeeee..eeee..........eeeee....eeeeee..eeeeeeeeeeeee..........eeeee..eeeeeeeeeeeeee.hhh.eeee..eee..........eeeee.........eeeee......eee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b90 A 119 SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:226
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338      
         O50325_DICCH   119 SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eee....ee..............eeee..eeeeeee........eeeee.eeeeeeeee.......eee...eeeee..eeee..........eeeee....eeeeee..eeeeeeeeeeee...ee......eeeee..eeeeeeeeeeeeee.hhh.eeee..eee..........eeeee.ee......eeeee......eee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b90 B 119 SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338

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 "SCOP Domain" information available for 3B90)

(no "CATH Domain" information available for 3B90)

(no "Pfam Domain" information available for 3B90)

Asymmetric Unit(hide GO term definitions)

Chain A,B (O50325_DICCH | O50325)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030570	pectate lyase activity	Catalysis of the reaction: a pectate = a pectate + a pectate oligosaccharide with 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate end. This reaction is the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
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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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
		Gly A:262 - Pro A:263	[ RasMol ]
		Gly B:262 - Pro B:263	[ RasMol ]
		Lys A:305 - Pro A:306	[ RasMol ]
		Lys B:305 - Pro B:306	[ RasMol ]

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		Biological Unit 4	[ Jena3D ]

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	O50325_DICCH \| O50325	:	3b4n 3b8y

3b4n	THE UNLIGANDED STRUCTURE OF PECTATE LYASE PELI.
3b8y

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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Gene Ontology (4, 4)

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