1DXE - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA COLI

Authors :   T. Izard, N. C. Blackwell

Date :   03 Jan 00 (Deposition) - 25 Aug 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	12	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:24 , ARG A:75 , GLN A:151 , GLU A:153 , PHE A:174 , GLY A:176 , PRO A:177 , LEU A:216 , PO4 A:302 , MG A:901 , HOH A:2192 , HOH A:2240 , HOH A:2326	BINDING SITE FOR RESIDUE PO4 A 301
2	AC2	SOFTWARE	SER A:124 , VAL A:125 , LEU A:216 , PO4 A:301 , HOH A:2078 , HOH A:2240 , HOH A:2327 , HOH A:2328 , HOH A:2329	BINDING SITE FOR RESIDUE PO4 A 302
3	AC3	SOFTWARE	GLU A:153 , ASP A:179 , PO4 A:301 , HOH A:2081 , HOH A:2192 , HOH A:2326	BINDING SITE FOR RESIDUE MG A 901
4	AC4	SOFTWARE	TRP B:24 , ARG B:75 , GLN B:151 , GLU B:153 , PHE B:174 , GLY B:176 , PRO B:177 , LEU B:216 , PO4 B:302 , MG B:901 , HOH B:2186 , HOH B:2228 , HOH B:2322	BINDING SITE FOR RESIDUE PO4 B 301
5	AC5	SOFTWARE	SER B:124 , VAL B:125 , LEU B:216 , PO4 B:301 , HOH B:2084 , HOH B:2228 , HOH B:2323 , HOH B:2324 , HOH B:2325	BINDING SITE FOR RESIDUE PO4 B 302
6	AC6	SOFTWARE	GLU B:153 , ASP B:179 , PO4 B:301 , HOH B:2086 , HOH B:2186 , HOH B:2322	BINDING SITE FOR RESIDUE MG B 901

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

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 1DXE)

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

(no "Exon" information available for 1DXE)

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 d1dxea_ A: 2-dehydro-3-deoxy-galactarate aldolase                                                                                                                                                                                                             SCOP domains
               CATH domains 1dxeA00 A:4-256 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...eeeeee...hhhhhhhhh.....eeeee......hhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhh..............hhhhh.....hhhhhhh...eeeeee.hhhhhhhhhhhhh.....eeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxe 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

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 d1dxeb_ B: 2-dehydro-3-deoxy-galactarate aldolase                                                                                                                                                                                                             SCOP domains
               CATH domains 1dxeB00 B:4-256 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...eeeeee...hhhhhhhhh.....eeeee......hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh..eeee....hhhhhhhhhhh..............hhhhh.....hhhhhhh...eeeeee.hhhhhhhhhhhhh.....eeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxe 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

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	d1dxea_	A:
1b	d1dxeb_	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	1dxeA00	A:4-256
1b	1dxeB00	B:4-256

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

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1dxe
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GARL_ECOLI \| P23522
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.2.20
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GARL_ECOLI \| P23522
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GARL_ECOLI \| P23522	:	1dxf

1dxf	2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE FROM ESCHERICHIA COLI IN COMPLEX WITH PYRUVATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File