1DXF - JenaLib

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Title :   2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA COLI IN COMPLEX WITH PYRUVATE

Authors :   T. Izard, N. C. Blackwell

Date :   05 Jan 00 (Deposition) - 25 Aug 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Class Ii Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Izard, N. C. Blackwell
Crystal Structures Of The Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest A Novel Reaction Mechanism.
Embo J. V. 19 3849 2000
PubMed-ID: 10921867 | Reference-DOI: 10.1093/EMBOJ/19.15.3849

Molecule 1 - 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
	Chains	:	A, B
	EC Number	:	4.1.2.20
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PYR	2	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	PYR	6	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:153 , ASP A:179 , PYR A:501 , HOH A:2027 , HOH A:2073	BINDING SITE FOR RESIDUE MG A 901
2	AC2	SOFTWARE	GLU B:153 , ASP B:179 , PYR B:501 , HOH B:2034 , HOH B:2079	BINDING SITE FOR RESIDUE MG B 901
3	AC3	SOFTWARE	ARG A:75 , GLN A:151 , GLU A:153 , GLY A:176 , PRO A:177 , SER A:178 , ASP A:179 , LEU A:216 , MG A:901	BINDING SITE FOR RESIDUE PYR A 501
4	AC4	SOFTWARE	ARG B:75 , GLN B:151 , GLU B:153 , PHE B:174 , GLY B:176 , PRO B:177 , SER B:178 , ASP B:179 , LEU B:216 , MG B:901	BINDING SITE FOR RESIDUE PYR B 501

(no "SS Bond" information available for 1DXF)

Asymmetric Unit

No.	Residues
1	Phe A:6	-	Pro A:7
2	Pro A:116	-	Pro A:117
3	Phe B:6	-	Pro B:7
4	Pro B:116	-	Pro B:117

(no "SAP(SNP)/Variant" information available for 1DXF)

(no "PROSITE Motif" information available for 1DXF)

(no "Exon" information available for 1DXF)

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:253
 aligned with GARL_ECOLI | P23522 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:253
                                    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   
           GARL_ECOLI     4 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSATQKLADTFKK 256
               SCOP domains d1dxfa_ A: 2-dehydro-3-deoxy-galactarate aldolase                                                                                                                                                                                                             SCOP domains
               CATH domains 1dxfA00 A:4-256 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...eeeeee...hhhhhhhhh.....eeeee......hhhhhhhhh........eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh.......................hhhhhhh...eeeeee.hhhhhhhhhhhhhh..eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxf A   4 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLmALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANmFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSATQKLADTFKK 256
                                    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   
                                                                                      63-MSE                                                             131-MSE

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with GARL_ECOLI | P23522 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:253
                                    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   
           GARL_ECOLI     4 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSATQKLADTFKK 256
               SCOP domains d1dxfb_ B: 2-dehydro-3-deoxy-galactarate aldolase                                                                                                                                                                                                             SCOP domains
               CATH domains 1dxfB00 B:4-256 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...eeeeee...hhhhhhhhh.....eeeee......hhhhhhhhh........eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh.......................hhhhhhh...eeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxf B   4 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLmALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANmFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSATQKLADTFKK 256
                                    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   
                                                                                      63-MSE                                                             131-MSE

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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Phosphoenolpyruvate/pyruvate domain (92)

Family: HpcH/HpaI aldolase (7)

Protein domain: 2-dehydro-3-deoxy-galactarate aldolase (2)

Escherichia coli [TaxId: 562] (2)

1a	d1dxfa_	A:
1b	d1dxfb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Phosphoenolpyruvate-binding domains (67)

Escherichia coli. Organism_taxid: 562 (3)

1a	1dxfA00	A:4-256
1b	1dxfB00	B:4-256

(no "Pfam Domain" information available for 1DXF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GARL_ECOLI | P23522)

molecular function
	GO:0008672	2-dehydro-3-deoxyglucarate aldolase activity	Catalysis of the reaction: 2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.
	GO:0016830	carbon-carbon lyase activity	Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
	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:0042838	D-glucarate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-glucarate, the D-enantiomer of glucarate.
	GO:0046392	galactarate catabolic process	The chemical reactions and pathways resulting in the breakdown of galactarate, the anion of galactaric acid.
	GO:0019394	glucarate catabolic process	The chemical reactions and pathways resulting in the breakdown of glucarate, the anion of glucaric acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:6 - Pro A:7	[ RasMol ]
		Phe B:6 - Pro B:7	[ RasMol ]
		Pro A:116 - Pro A:117	[ RasMol ]
		Pro B:116 - Pro B:117	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	GARL_ECOLI \| P23522	:	1dxe

1dxe	2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (10, 10)

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