3LMW - JenaLib

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Title :   CRYSTAL STRUCTURE OF IOTA-CARRAGEENASE FAMILY GH82 FROM A. FORTIS IN ABSENCE OF CHLORIDE IONS

Authors :   E. Rebuffet, T. Barbeyron, A. Jeudy, M. Czjzek, G. Michel

Date :   01 Feb 10 (Deposition) - 18 Aug 10 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Iota-Carrageenase, Marine Bacterial Enzyme, Family Gh82, Glycoside Hydrolase, Beta-Helix Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Rebuffet, T. Barbeyron, A. Jeudy, M. Jam, M. Czjzek, G. Michel
Identification Of Catalytic Residues And Mechanistic Analysis Of Family Gh82 Iota-Carrageenases
Biochemistry V. 49 7590 2010
PubMed-ID: 20681629 | Reference-DOI: 10.1021/BI1003475

Molecule 1 - IOTA-CARRAGEENASE, CGIA
	Chains	:	A, B
	EC Number	:	3.2.1.157
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CGIA
	Organism Scientific	:	ALTEROMONAS
	Organism Taxid	:	116059
	Strain	:	ATCC 43554

		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, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NI	1	Ligand/Ion	NICKEL (II) ION
3	NO3	4	Ligand/Ion	NITRATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	NO3	3	Ligand/Ion	NITRATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:217 , ARG A:243 , LEU A:273 , ARG A:303 , LYS A:394	BINDING SITE FOR RESIDUE NO3 A 3
2	AC2	SOFTWARE	ASN A:58 , ASP A:61 , SER A:63 , ASP A:65	BINDING SITE FOR RESIDUE CA A 9
3	AC3	SOFTWARE	ASP A:178 , HIS A:496 , HIS A:498 , HOH A:658	BINDING SITE FOR RESIDUE NI A 1
4	AC4	SOFTWARE	ARG B:243 , LEU B:273 , ARG B:303 , LYS B:394	BINDING SITE FOR RESIDUE NO3 B 1
5	AC5	SOFTWARE	HIS A:235 , ARG A:268 , ASN B:89 , GLU B:108 , SER B:109 , ASP B:110	BINDING SITE FOR RESIDUE NO3 B 2
6	AC6	SOFTWARE	ARG B:303 , LYS B:394 , ASP B:396 , GLN B:397	BINDING SITE FOR RESIDUE NO3 B 6

Asymmetric Unit

No.	Residues
1	A:269	-	A:298
2	A:336	-	A:360
3	A:408	-	A:476
4	A:412	-	A:484
5	B:269	-	B:298
6	B:336	-	B:360
7	B:408	-	B:476
8	B:412	-	B:484

(no "Cis Peptide Bond" information available for 3LMW)

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

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

(no "Exon" information available for 3LMW)

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:472
 aligned with CGIA_ALTFO | Q9F5I8 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         491        
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487   |     -  
           CGIA_ALTFO    28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........eeeehhhhhh........hhhhhhhhhhhhhhh...eeeee...eeee..ee....eeeee....eeee........eeeee.........eeeee....eeee........eeeeee.....eeeeeeeee........eee..eee..eee....eeeeeeeee......eeeee.eeeeeeeeeeeee..eeeeee..hhhhhhhh..eeeeeeeeeeeee...eeeeee........eeeeeeeee.....eee.....eee.......hhhhhhhhhhhhhh.......ee.......eeee...hhhhhhhhhhhhh........eeeeeeeee....eeehhhhhhhhh.......................eee.....eee...........eeeeeeeee........eee.................hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lmw A  28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWERLEHHHHHH 499
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497

Chain B from PDB  Type:PROTEIN  Length:449
 aligned with CGIA_ALTFO | Q9F5I8 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          491   
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    |   
           CGIA_ALTFO    27 AVSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------Pectate_lyase_3-3lmwB01 B:49-279                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------Pectate_lyase_3-3lmwB02 B:49-279                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhh........eeeehhhhhh........hhhhhhhhhhhhhhh...eeeee..eeeee..ee....eeeee...eeeee........eeeeee.....eeeeeeee....eeee........eeeeee..eeeeeeeeeeee........eee..eee..eee.eeeeeeeeeeee......eeeee.eeeeeeeeeeeee..eeeeee..hhhhhhhh..eeeeeeeeeeeee...eeeeee........eeeeeeeee.....eeee....ee--------hhhhhhhhhh---..........--------.ee...hhhhhhhhhhhhh........eeeeeeeee....eeehhhhhhhhh.......................eee.....eeee..........eee..eeee........eee.................hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lmw B  27 AVSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVEL--------TRQSWKQAVE---GRGCAQTPYA--------AARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWERLEH 494
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306    |    -   |   326  |   |336     |   -    |  356       366       376       386       396       406       416       426       436       446       456       466       476       486        
                                                                                                                                                                                                                                                                                                                      311      320      329 333      342      351

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 3LMW)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Pec_lyase (42)

Family: Pectate_lyase_3 (5)

Alteromonas fortis (Alteromonas sp. (strain ATCC 43554)) (2)

1a	Pectate_lyase_3-3lmwB01	B:49-279
1b	Pectate_lyase_3-3lmwB02	B:49-279

Asymmetric Unit(hide GO term definitions)

Chain A,B (CGIA_ALTFO | Q9F5I8)

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:0033952	iota-carrageenase activity	Catalysis of the endohydrolysis of 1,4-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose-2-sulfate in iota-carrageenans.
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.
	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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lmw)

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

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Access by PDB/NDB ID
	3lmw
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	3.2.1.157
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UniProtKB/Swiss-Prot
	CGIA_ALTFO \| Q9F5I8	:	1h80 1ktw

1h80	WILD-TYPE CRYSTAL STRUCTURE OF IOTA-CARRAGEENASE
1ktw	COMPLEX CRYSTAL STRUCTURE OF IOTA-CARRAGEENASE WITH OLIGO- IOTA-CARRAGEENAN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (9, 9)

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