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Title :   SCHIFF BASE INTERMEDIATE IN KDPG ALDOLASE FROM ESCHERICHIA COLI

Authors :   J. Allard, P. Grochulski, J. Sygusch

Date :   14 Apr 00 (Deposition) - 07 Feb 01 (Release) - 21 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Beta Barrel, Trimer, Carbinolamine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Allard, P. Grochulski, J. Sygusch
Covalent Intermediate Trapped In 2-Keto-3-Deoxy-6- Phosphogluconate (Kdpg) Aldolase Structure At 1. 95-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 98 3679 2001
PubMed-ID: 11274385 | Reference-DOI: 10.1073/PNAS.071380898

Molecule 1 - KDPG ALDOLASE
	Chains	:	A, B, C
	EC Number	:	4.1.2.14
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	PYR	3	Ligand/Ion	PYRUVIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:96 , HOH A:2380 , SER B:119	BINDING SITE FOR RESIDUE ACT A 2001
2	AC2	SOFTWARE	VAL A:23 , LYS A:24 , LYS A:25 , HIS A:28 , LEU A:192 , HOH A:2309	BINDING SITE FOR RESIDUE ACT A 2002
3	AC3	SOFTWARE	GLY B:162 , GLY B:163 , SER B:184 , HOH B:2226 , HOH B:2257 , HOH B:2340 , HOH B:2351 , HOH B:2444	BINDING SITE FOR RESIDUE SO4 B 2201
4	AC4	SOFTWARE	GLY A:162 , GLY A:163 , SER A:184 , HOH A:2248 , HOH A:2299 , HOH A:2326 , HOH A:2376	BINDING SITE FOR RESIDUE SO4 A 2202
5	AC5	SOFTWARE	GLY C:162 , GLY C:163 , SER C:184 , HOH C:2205 , HOH C:2234 , HOH C:2265 , HOH C:2333	BINDING SITE FOR RESIDUE SO4 C 2203
6	AC6	SOFTWARE	VAL A:20 , GLU A:45 , ARG A:49 , GLY A:72 , THR A:73 , ILE A:92 , SER A:93 , PRO A:94 , LYS A:133	BINDING SITE FOR RESIDUE PYR A 2101
7	AC7	SOFTWARE	GLU B:45 , ARG B:49 , THR B:73 , ILE B:92 , SER B:93 , PRO B:94 , LYS B:133 , HOH B:2244	BINDING SITE FOR RESIDUE PYR B 2102
8	AC8	SOFTWARE	GLU C:45 , ARG C:49 , GLY C:72 , THR C:73 , ILE C:92 , SER C:93 , PRO C:94 , LYS C:133	BINDING SITE FOR RESIDUE PYR C 2103

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:135	-	Pro A:136
2	Phe B:135	-	Pro B:136
3	Phe C:135	-	Pro C:136

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

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOLASE_KDPG_KHG_1	PS00159	KDPG and KHG aldolases active site.	ALKH_ECOLI	40-49	3	A:40-49 B:40-49 C:40-49
2	ALDOLASE_KDPG_KHG_2	PS00160	KDPG and KHG aldolases Schiff-base forming residue.	ALKH_ECOLI	128-141	3	A:128-141 B:128-141 C:128-141

(no "Exon" information available for 1EUA)

Asymmetric/Biological 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:213
 aligned with ALKH_ECOLI | P0A955 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           ALKH_ECOLI     1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
               SCOP domains d1euaa_ A: KDPG aldolase                                                                                                                                                                                              SCOP domains
               CATH domains 1euaA00 A:1-213 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..eeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...eee...hhhhhhhhhhh...eeeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh......eeee.......hhhhhhh......eee....hhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------ALDOLASE_K------------------------------------------------------------------------------ALDOLASE_KDPG_------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eua A   1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with ALKH_ECOLI | P0A955 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           ALKH_ECOLI     1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
               SCOP domains d1euab_ B: KDPG aldolase                                                                                                                                                                                              SCOP domains
               CATH domains 1euaB00 B:1-213 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..eeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhh....eee...hhhhhhhhhhh...eeeee.hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eee....hhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------ALDOLASE_K------------------------------------------------------------------------------ALDOLASE_KDPG_------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eua B   1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with ALKH_ECOLI | P0A955 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           ALKH_ECOLI     1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
               SCOP domains d1euac_ C: KDPG aldolase                                                                                                                                                                                              SCOP domains
               CATH domains 1euaC00 C:1-213 Aldolase class I                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..eeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhh....eee...hhhhhhhhhhh...eeeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh......eeee.......hhhhhhh......eee....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------ALDOLASE_K------------------------------------------------------------------------------ALDOLASE_KDPG_------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eua C   1 MKNWKTSAESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVPADALEAGDYDRITKLAREAVEGAKL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class I aldolase (182)

Protein domain: KDPG aldolase (9)

Escherichia coli [TaxId: 562] (7)

1a	d1euaa_	A:
1b	d1euab_	B:
1c	d1euac_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562 (6)

1a	1euaA00	A:1-213
1b	1euaB00	B:1-213
1c	1euaC00	C:1-213

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (ALKH_ECOLI | P0A955)

molecular function
	GO:0008675	2-dehydro-3-deoxy-phosphogluconate aldolase activity	Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.
	GO:0008700	4-hydroxy-2-oxoglutarate aldolase activity	Catalysis of the reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Phe A:135 - Pro A:136	[ RasMol ]
		Phe B:135 - Pro B:136	[ RasMol ]
		Phe C:135 - Pro C:136	[ RasMol ]

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	1eua
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	4.1.2.14
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	ALKH_ECOLI \| P0A955	:	1eun 1fq0 1fwr 1wau 1wbh 2c0a

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

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Exons (0, 0)

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