2PP0 - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L-TALARATE/GALACTARATE DEHYDRATASE FROM SALMONELLA TYPHIMURIUM LT2

Authors :   A. A. Fedorov, E. V. Fedorov, W. S. Yew, J. A. Gerlt, S. C. Almo

Date :   27 Apr 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: B,C  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B,C  (3x)
Biol. Unit 4: A  (6x)
Biol. Unit 5: A  (8x)
Biol. Unit 6: B,C  (4x)

Keywords :   Enolase Superfamily, L-Talarate/Galactarate Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. S. Yew, A. A. Fedorov, E. V. Fedorov, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: L-Talarate/Galactarate Dehydratase From Salmonella Typhimurium Lt2.
Biochemistry V. 46 9564 2007
PubMed-ID: 17649980 | Reference-DOI: 10.1021/BI7008882

Molecule 1 - L-TALARATE/GALACTARATE DEHYDRATASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:		B	C
Biological Unit 2 (2x)	:	A
Biological Unit 3 (3x)	:		B	C
Biological Unit 4 (6x)	:	A
Biological Unit 5 (8x)	:	A
Biological Unit 6 (4x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL

Biological Unit 4 (1, 6)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL

Biological Unit 5 (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 6 (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:46 , LYS A:82 , LYS A:197 , ASN A:228 , GLU A:278 , HIS A:328 , HOH A:642 , HOH A:730	BINDING SITE FOR RESIDUE GOL A 601
2	AC2	SOFTWARE	ASP B:46 , LYS B:82 , PHE B:171 , LYS B:197 , ASN B:228 , GLU B:278 , HIS B:328	BINDING SITE FOR RESIDUE GOL B 602
3	AC3	SOFTWARE	ASP C:46 , LYS C:82 , LYS C:197 , ASN C:228 , GLU C:278 , HIS C:328 , HOH C:700 , HOH C:722	BINDING SITE FOR RESIDUE GOL C 603

(no "SS Bond" information available for 2PP0)

(no "Cis Peptide Bond" information available for 2PP0)

(no "SAP(SNP)/Variant" information available for 2PP0)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	3	A:223-254 B:223-254 C:223-254

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	2	- B:223-254 C:223-254

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	2	A:223-254 - -

Biological Unit 3 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	6	- B:223-254 C:223-254

Biological Unit 4 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	6	A:223-254 - -

Biological Unit 5 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	8	A:223-254 - -

Biological Unit 6 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	TAGAD_SALTY	223-254	8	- B:223-254 C:223-254

(no "Exon" information available for 2PP0)

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:395
 aligned with TAGAD_SALTY | Q8ZL58 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:395
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
          TAGAD_SALTY     4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------2pp0A01 A:19-148,A:382-398 Enolase-like, N-terminal domain                                                                        2pp0A02 A:149-381 Enolase superfamily                                                                                                                                                                                                    2pp0A01           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhh..eeeeeeeeeeeeeeeee.hhhhhh.....eeeeeeeeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhh......eee...hhhhh....eee..eee...........hhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_2  PDB: A:223-254        ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pp0 A   4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with TAGAD_SALTY | Q8ZL58 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:395
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
          TAGAD_SALTY     4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------2pp0B01 B:19-148,B:382-398 Enolase-like, N-terminal domain                                                                        2pp0B02 B:149-381 Enolase superfamily                                                                                                                                                                                                    2pp0B01           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhh..eeeeeeeeeeeeeeeee.hhhhhh.....eeeeeeeeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee.hhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhh.....eeee...hhhhh....eee..eee...........hhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_2  PDB: B:223-254        ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pp0 B   4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393

Chain C from PDB  Type:PROTEIN  Length:395
 aligned with TAGAD_SALTY | Q8ZL58 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:395
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
          TAGAD_SALTY     4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------2pp0C01 C:19-148,C:382-398 Enolase-like, N-terminal domain                                                                        2pp0C02 C:149-381 Enolase superfamily                                                                                                                                                                                                    2pp0C01           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhh..eeeeeeeeeeeeeeeee.hhhhhh.....eeeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....eeeeee........hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhh......eee...hhhhh....eee..eee...........hhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_2  PDB: C:223-254        ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pp0 C   4 SANSDAVTYAKAANTRTAAETGDRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTLSEQARRWTQLTCEFGKRP 398
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393

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 2PP0)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: Enolase-like, N-terminal domain (130)

Salmonella typhimurium. Organism_taxid: 602. (3)

1a	2pp0A01	A:19-148,A:382-398
1b	2pp0B01	B:19-148,B:382-398
1c	2pp0C01	C:19-148,C:382-398

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Enolase superfamily (142)

Salmonella typhimurium. Organism_taxid: 602. (3)

2a	2pp0A02	A:149-381
2b	2pp0B02	B:149-381
2c	2pp0C02	C:149-381

(no "Pfam Domain" information available for 2PP0)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (TAGAD_SALTY | Q8ZL58)

molecular function
	GO:1990594	L-altrarate dehydratase activity	Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
	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:0008867	galactarate dehydratase activity	Catalysis of the reaction: galactarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
	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.
biological process
	GO:1903663	L-altrarate catabolic process	The chemical reactions and pathways resulting in the breakdown of L-altrarate.
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
	GO:0046392	galactarate catabolic process	The chemical reactions and pathways resulting in the breakdown of galactarate, the anion of galactaric acid.
	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.

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(no "Cis Peptide Bonds" information available for 2pp0)

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	2pp0
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UniProtKB/Swiss-Prot
	TAGAD_SALTY \| Q8ZL58	:	2pp1 2pp3

2pp1	THE SAME PROTEIN COMPLEXED WITH MG AND L-LYXAROHYDROXAMATE
2pp3	THE SAME PROTEIN COMPLEXED WITH MG AND L-GLUCARATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Related Entries

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Related Entries Specified in the PDB File