2DW6 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MUTANT K184A OF D-TARTRATE DEHYDRATASE FROM BRADYRHIZOBIUM JAPONICUM COMPLEXED WITH MG++ AND D-TARTRATE

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

Date :   07 Aug 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   W. S. Yew, A. A. Fedorov, E. V. Fedorov, B. M. Wood, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: D-Tartrate Dehydratase From Bradyrhizobium Japonicum
Biochemistry V. 45 14598 2006
PubMed-ID: 17144653 | Reference-DOI: 10.1021/BI061688G
(for further references see the PDB file header)

Molecule 1 - BLL6730 PROTEIN
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.81
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	BRADYRHIZOBIUM JAPONICUM
	Organism Taxid	:	375
	Synonym	:	D-TARTRATE DEHYDRATASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	TAR	3	Ligand/Ion	D(-)-TARTARIC ACID
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID
3	TLA	-1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:213 , GLU A:239 , GLU A:265 , TAR A:1001 , HOH A:2002	BINDING SITE FOR RESIDUE MG A 2001
2	AC2	SOFTWARE	ASP B:213 , GLU B:239 , GLU B:265 , TAR B:1002 , HOH B:2003	BINDING SITE FOR RESIDUE MG B 2002
3	AC3	SOFTWARE	ASP C:213 , GLU C:239 , GLU C:265 , TAR C:1003 , HOH C:2004	BINDING SITE FOR RESIDUE MG C 2003
4	AC4	SOFTWARE	LYS D:182 , ASP D:213 , GLU D:239 , GLU D:265 , TLA D:1004 , HOH D:2005	BINDING SITE FOR RESIDUE MG D 2004
5	AC5	SOFTWARE	LYS C:102 , ASN D:21 , PHE D:26 , TYR D:156 , LYS D:182 , ASP D:213 , ASN D:215 , GLU D:239 , GLU D:265 , HIS D:322 , GLU D:341 , TYR D:343 , MG D:2004 , HOH D:2005 , HOH D:2112	BINDING SITE FOR RESIDUE TLA D 1004
6	AC6	SOFTWARE	ASN A:21 , PHE A:26 , ASN A:55 , TYR A:156 , LYS A:182 , ASP A:213 , ASN A:215 , GLU A:239 , GLU A:265 , HIS A:322 , GLU A:341 , TYR A:343 , MG A:2001 , HOH A:2002 , LYS B:102	BINDING SITE FOR RESIDUE TAR A 1001
7	AC7	SOFTWARE	LYS A:102 , ASN B:21 , PHE B:26 , ASN B:55 , TYR B:156 , LYS B:182 , ASP B:213 , ASN B:215 , GLU B:239 , GLU B:265 , HIS B:322 , GLU B:341 , TYR B:343 , MG B:2002 , HOH B:2003 , HOH B:2073	BINDING SITE FOR RESIDUE TAR B 1002
8	AC8	SOFTWARE	ASN C:21 , PHE C:26 , ASN C:55 , TYR C:156 , LYS C:182 , ASP C:213 , ASN C:215 , GLU C:239 , GLU C:265 , HIS C:322 , GLU C:341 , TYR C:343 , MG C:2003 , HOH C:2004 , HOH C:2040 , LYS D:102	BINDING SITE FOR RESIDUE TAR C 1003

(no "SS Bond" information available for 2DW6)

Asymmetric Unit

No.	Residues
1	Gln A:348	-	Pro A:349
2	Gln B:348	-	Pro B:349
3	Gln C:348	-	Pro C:349
4	Gln D:348	-	Pro D:349

(no "SAP(SNP)/Variant" information available for 2DW6)

(no "PROSITE Motif" information available for 2DW6)

(no "Exon" information available for 2DW6)

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:388
 aligned with TARD_BRADU | Q89FH0 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
           TARD_BRADU     2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMKIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
               SCOP domains d2dw6a2 A:2-142 automated matches                                                                                                            d2dw6a1 A:143-389 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2dw6A01 A:2-129 Enolase-like, N-terminal domain                                                                                 2dw6A02 A:130-389 Enolase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee...............eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.....eee......hhhhhhhhh......eee.....hhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhh...eee....................eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dw6 A   2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Chain B from PDB  Type:PROTEIN  Length:388
 aligned with TARD_BRADU | Q89FH0 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
           TARD_BRADU     2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMKIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
               SCOP domains d2dw6b2 B:2-142 automated matches                                                                                                            d2dw6b1 B:143-389 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2dw6B01 B:2-129 Enolase-like, N-terminal domain                                                                                 2dw6B02 B:130-389 Enolase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee...............eeeeeeeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.....eee......hhhhhhhhh......eee.....hhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhh...eee....................eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dw6 B   2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Chain C from PDB  Type:PROTEIN  Length:388
 aligned with TARD_BRADU | Q89FH0 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
           TARD_BRADU     2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMKIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
               SCOP domains d2dw6c2 C:2-142 automated matches                                                                                                            d2dw6c1 C:143-389 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2dw6C01 C:2-129 Enolase-like, N-terminal domain                                                                                 2dw6C02 C:130-389 Enolase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee...............eeeeeeeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.....eee......hhhhhhhhh......eee.....hhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhh...eee....................eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dw6 C   2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

Chain D from PDB  Type:PROTEIN  Length:388
 aligned with TARD_BRADU | Q89FH0 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
           TARD_BRADU     2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMKIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
               SCOP domains d2dw6d2 D:2-142 automated matches                                                                                                            d2dw6d1 D:143-389 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2dw6D01 D:2-129 Enolase-like, N-terminal domain                                                                                 2dw6D02 D:130-389 Enolase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....ee..ee....eeeeeeeeeeeee..eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee......hhhhhhhhh......eee.....hhhhhhhhhhhh.......ee.......hhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhh...eee....................eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dw6 D   2 SVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE 389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Enolase N-terminal domain-like (211)

Superfamily: Enolase N-terminal domain-like (211)

Family: automated matches (123)

Protein domain: automated matches (123)

Bradyrhizobium japonicum [TaxId: 375] (2)

1a	d2dw6a2	A:2-142
1b	d2dw6b2	B:2-142
1c	d2dw6c2	C:2-142
1d	d2dw6d2	D:2-142

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Enolase C-terminal domain-like (212)

Family: D-glucarate dehydratase-like (65)

Protein domain: automated matches (16)

Bradyrhizobium japonicum [TaxId: 375] (2)

2a	d2dw6a1	A:143-389
2b	d2dw6b1	B:143-389
2c	d2dw6c1	C:143-389
2d	d2dw6d1	D:143-389

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)

Bradyrhizobium japonicum. Organism_taxid: 375. (3)

1a	2dw6A01	A:2-129
1b	2dw6B01	B:2-129
1c	2dw6C01	C:2-129
1d	2dw6D01	D:2-129

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Enolase superfamily (142)

Bradyrhizobium japonicum. Organism_taxid: 375. (3)

2a	2dw6A02	A:130-389
2b	2dw6B02	B:130-389
2c	2dw6C02	C:130-389
2d	2dw6D02	D:130-389

(no "Pfam Domain" information available for 2DW6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TARD_BRADU | Q89FH0)

molecular function
	GO:0047808	D(-)-tartrate dehydratase activity	Catalysis of the reaction: D-tartrate = H(2)O + oxaloacetate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gln A:348 - Pro A:349	[ RasMol ]
		Gln B:348 - Pro B:349	[ RasMol ]
		Gln C:348 - Pro C:349	[ RasMol ]
		Gln D:348 - Pro D:349	[ RasMol ]

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Access by PDB/NDB ID
	2dw6
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	4.2.1.81
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	TARD_BRADU \| Q89FH0
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UniProtKB/Swiss-Prot
	TARD_BRADU \| Q89FH0	:	1tzz 2dw7

1tzz	THE SAME WILD TYPE PROTEIN LIGANDED WITH MG++
2dw7	THE SAME WILD TYPE PROTEIN COMPLEXED WITH MG++ AND S,R MESO -TARTARIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (2, 8)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File