3B4N - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF PECTATE LYASE PELI FROM ERWINIA CHRYSANTHEMI

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

Date :   24 Oct 07 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Pectate Lyase, Pectin, Galacturonic Acid, Erwinia Chrysanthemi, Right-Handed Parallel Beta Helix Fold (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
(for further references see the PDB file header)

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

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

Biological Unit 2 (2, 5)

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

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP B:191 , ILE B:192 , ASN B:213 , TYR B:218 , HOH B:1383 , HOH B:1384 , HOH B:1731	BINDING SITE FOR RESIDUE CA B 701
02	AC2	SOFTWARE	ASP A:191 , ILE A:192 , ASN A:213 , TYR A:218 , HOH A:1003 , HOH A:1026	BINDING SITE FOR RESIDUE CA A 702
03	AC3	SOFTWARE	ASP A:173 , ASP A:195 , HOH A:1385 , HOH A:1386	BINDING SITE FOR RESIDUE ZN A 711
04	AC4	SOFTWARE	ASP A:148 , HOH A:1387 , HIS B:176 , ASP B:178	BINDING SITE FOR RESIDUE ZN B 712
05	AC5	SOFTWARE	ASP B:173 , ASP B:195 , HOH B:1388 , HOH B:1389	BINDING SITE FOR RESIDUE ZN B 713
06	AC6	SOFTWARE	HIS A:176 , ASP A:178 , HOH A:1390	BINDING SITE FOR RESIDUE ZN A 714
07	AC7	SOFTWARE	ASP A:146 , ASP B:173 , HIS B:176 , HOH B:1389	BINDING SITE FOR RESIDUE ZN B 715
08	AC8	SOFTWARE	ASP A:173 , HIS A:176 , THR A:198 , HOH A:1385	BINDING SITE FOR RESIDUE ZN A 716
09	AC9	SOFTWARE	LYS B:224 , LYS B:249 , ARG B:252 , HOH B:1633 , HOH B:1639	BINDING SITE FOR RESIDUE SO4 B 721
10	BC1	SOFTWARE	GLN A:21 , THR A:23 , SER A:38 , THR A:39 , ASP A:133 , LYS A:162 , ASN A:163	BINDING SITE FOR RESIDUE EDO A 801
11	BC2	SOFTWARE	GLU B:69 , ARG B:71 , GLY B:239 , HOH B:1255	BINDING SITE FOR RESIDUE EDO B 802
12	BC3	SOFTWARE	PRO A:57 , ARG A:60 , HOH A:1414	BINDING SITE FOR RESIDUE EDO A 803
13	BC4	SOFTWARE	GLN B:21 , THR B:23 , SER B:38 , THR B:39 , ASP B:40 , ASP B:133 , ASN B:163	BINDING SITE FOR RESIDUE EDO B 804
14	BC5	SOFTWARE	ARG A:62 , ILE A:63 , ALA A:64 , HOH A:1105 , HOH B:1220	BINDING SITE FOR RESIDUE EDO A 805
15	BC6	SOFTWARE	LYS A:202 , THR A:203 , ASN A:232 , SER A:233 , THR A:234 , ASN B:94 , GLN B:95	BINDING SITE FOR RESIDUE EDO B 806
16	BC7	SOFTWARE	THR B:131 , ASN B:158 , ALA B:159 , THR B:160 , HOH B:1599 , HOH B:1602	BINDING SITE FOR RESIDUE EDO B 807

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 3B4N)

(no "PROSITE Motif" information available for 3B4N)

(no "Exon" information available for 3B4N)

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:314
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:325
                                    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     
         O50325_DICCH    20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAPNAGPLRAAKASSECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b4nA01 A:20-107 Immunoglobulins                                                        -----------3b4nA02 A:119-344 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee....eeeeeeeee...hhhhheeeeee.....eeee.........eeeeeeee....eee...ee...-----------......eeee..eee....ee..............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
                 3b4n A  20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAP-----------SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                    29        39        49        59        69        79        89        99       | -       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                                                 107         119

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:325
                                    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     
         O50325_DICCH    20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAPNAGPLRAAKASSECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b4nB01 B:20-107 Immunoglobulins                                                        -----------3b4nB02 B:119-344 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee....eeeeeeeee...hhhhheeeeee.....eeee.........eeeeeeee....eee...ee...-----------......eeee..eee....ee..............eeee..eeeeeee........eeeee.eeeeeeeee.......eee...eeeee..eeee..........eeeee....eeeeee..eeeeeeeeeeeee..........eeeee..eee..eeeeeeeee.hhh.eeee..eee..........eeeee.........eeeee......eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b4n B  20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAP-----------SECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                    29        39        49        59        69        79        89        99       | -       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                                                 107         119

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 3B4N)

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)

Erwinia chrysanthemi. Organism_taxid: 556. (6)

1a	3b4nA02	A:119-344
1b	3b4nB02	B:119-344

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Erwinia chrysanthemi. Organism_taxid: 556. (2)

2a	3b4nA01	A:20-107
2b	3b4nB01	B:20-107

(no "Pfam Domain" information available for 3B4N)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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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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3b8y	CRYSTAL STRUCTURE OF PECTATE LYASE PELI FROM ERWINIA CHRYSANTHEMI IN COMPLEX WITH TETRAGALACTURONIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

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