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(-) Description

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

(-) Compounds

Molecule 1 - KDPG ALDOLASE
    ChainsA, B, C
    EC Number4.1.2.14
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2PYR3Ligand/IonPYRUVIC ACID
3SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:96 , HOH A:2380 , SER B:119BINDING SITE FOR RESIDUE ACT A 2001
2AC2SOFTWAREVAL A:23 , LYS A:24 , LYS A:25 , HIS A:28 , LEU A:192 , HOH A:2309BINDING SITE FOR RESIDUE ACT A 2002
3AC3SOFTWAREGLY B:162 , GLY B:163 , SER B:184 , HOH B:2226 , HOH B:2257 , HOH B:2340 , HOH B:2351 , HOH B:2444BINDING SITE FOR RESIDUE SO4 B 2201
4AC4SOFTWAREGLY A:162 , GLY A:163 , SER A:184 , HOH A:2248 , HOH A:2299 , HOH A:2326 , HOH A:2376BINDING SITE FOR RESIDUE SO4 A 2202
5AC5SOFTWAREGLY C:162 , GLY C:163 , SER C:184 , HOH C:2205 , HOH C:2234 , HOH C:2265 , HOH C:2333BINDING SITE FOR RESIDUE SO4 C 2203
6AC6SOFTWAREVAL 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:133BINDING SITE FOR RESIDUE PYR A 2101
7AC7SOFTWAREGLU B:45 , ARG B:49 , THR B:73 , ILE B:92 , SER B:93 , PRO B:94 , LYS B:133 , HOH B:2244BINDING SITE FOR RESIDUE PYR B 2102
8AC8SOFTWAREGLU C:45 , ARG C:49 , GLY C:72 , THR C:73 , ILE C:92 , SER C:93 , PRO C:94 , LYS C:133BINDING SITE FOR RESIDUE PYR C 2103

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:135 -Pro A:136
2Phe B:135 -Pro B:136
3Phe C:135 -Pro C:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_KDPG_KHG_1PS00159 KDPG and KHG aldolases active site.ALKH_ECOLI40-49
 
 
  3A:40-49
B:40-49
C:40-49
2ALDOLASE_KDPG_KHG_2PS00160 KDPG and KHG aldolases Schiff-base forming residue.ALKH_ECOLI128-141
 
 
  3A:128-141
B:128-141
C:128-141

(-) Exons   (0, 0)

(no "Exon" information available for 1EUA)

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ALKH_ECOLI | P0A9551eun 1fq0 1fwr 1wau 1wbh 2c0a

(-) Related Entries Specified in the PDB File

1eun