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(-) Description

Title :  CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, HPAI, IN COMPLEX WITH PYRUVATE
 
Authors :  M. Coincon, W. Wang, S. Y. K. Seah, J. Sygusch
Date :  07 Aug 12  (Deposition) - 29 Aug 12  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Coincon, W. Wang, J. Sygusch, S. Y. K. Seah
Crystal Structure Of Reaction Intermediates In Pyruvate Class Ii Aldolase: Substrate Cleavage, Enolate Stabilizatio And Substrate Specificity
J. Biol. Chem. V. 287 36208 2012
PubMed-ID: 22908224  |  Reference-DOI: 10.1074/JBC.M112.400705

(-) Compounds

Molecule 1 - 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
    Atcc: 8739
    Chains: A, B
    EC Number: 4.1.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PT7-7
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-251
    Organism Scientific: ESCHERICHIA COLI ATCC 8739
    Organism Taxid: 481805
    Synonym: HPAI, 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE, HHED ALDOLASE, 4-HYDROXY-2-KETOHEPTANE-1,7-DIOATE ALDOLASE, HKHD ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
13GR1Ligand/IonGLYCERALDEHYDE
2CO2Ligand/IonCOBALT (II) ION
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5PO44Ligand/IonPHOSPHATE ION
6PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
13GR3Ligand/IonGLYCERALDEHYDE
2CO-1Ligand/IonCOBALT (II) ION
3GOL3Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5PO412Ligand/IonPHOSPHATE ION
6PYR6Ligand/IonPYRUVIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:22 , SER A:23 , PRO A:47 , 3GR A:1252 , HOH A:2147 , SER B:24 , TYR B:26 , HOH B:2093 , HOH B:2095 , HOH B:2497BINDING SITE FOR RESIDUE GOL B 1252
02AC2SOFTWARESER A:24 , TYR A:26 , HOH A:2092 , HOH A:2096 , HOH A:2525 , LEU B:22 , SER B:23 , PRO B:47 , GLN B:51 , LEU B:54 , GOL B:1252BINDING SITE FOR RESIDUE 3GR A 1252
03AC3SOFTWAREGLN A:147 , GLU A:149 , ASP A:175 , PYR A:1256 , HOH A:2140 , HOH A:2144BINDING SITE FOR RESIDUE CO A 1253
04AC4SOFTWAREVAL A:118 , SER A:120 , ALA A:121 , ASN A:129 , ALA A:174 , HOH A:2431 , HOH A:2434 , HOH A:2526 , HOH A:2527 , HOH A:2529BINDING SITE FOR RESIDUE PO4 A 1254
05AC5SOFTWARELYS A:10 , ALA A:11 , GLY A:12 , ARG A:203 , HOH A:2043 , HOH A:2463 , HOH A:2472 , HOH A:2530BINDING SITE FOR RESIDUE PO4 A 1255
06AC6SOFTWAREARG A:70 , GLN A:147 , GLU A:149 , PHE A:170 , GLY A:172 , PRO A:173 , ALA A:174 , ASP A:175 , LEU A:212 , CO A:1253 , MG A:1257 , HOH A:2144 , HOH A:2210 , HOH A:2528BINDING SITE FOR RESIDUE PYR A 1256
07AC7SOFTWAREGLN A:147 , GLU A:149 , ASP A:175 , PYR A:1256 , HOH A:2140 , HOH A:2144BINDING SITE FOR RESIDUE MG A 1257
08AC8SOFTWAREGLN B:147 , GLU B:149 , ASP B:175 , PYR B:1256 , HOH B:2143 , HOH B:2149BINDING SITE FOR RESIDUE CO B 1253
09AC9SOFTWAREVAL B:118 , GLY B:119 , SER B:120 , ALA B:121 , ASN B:129 , ALA B:174 , HOH B:2409 , HOH B:2410 , HOH B:2499 , HOH B:2500 , HOH B:2503BINDING SITE FOR RESIDUE PO4 B 1254
10BC1SOFTWAREGLY B:12 , ARG B:203 , HOH B:2051 , HOH B:2437BINDING SITE FOR RESIDUE PO4 B 1255
11BC2SOFTWAREARG B:70 , GLN B:147 , GLU B:149 , PHE B:170 , GLY B:172 , PRO B:173 , ALA B:174 , ASP B:175 , LEU B:212 , CO B:1253 , MG B:1257 , HOH B:2149 , HOH B:2215 , HOH B:2502BINDING SITE FOR RESIDUE PYR B 1256
12BC3SOFTWAREGLN B:147 , GLU B:149 , ASP B:175 , PYR B:1256 , HOH B:2143 , HOH B:2149BINDING SITE FOR RESIDUE MG B 1257

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:111 -Pro A:112
2Pro B:111 -Pro B:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5S)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5S)

(-) Sequences/Alignments

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:251
 aligned with HPCH_ECOLC | B1IS70 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           HPCH_ECOLC     1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFG 251
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5s A   1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFG 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with HPCH_ECOLC | B1IS70 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           HPCH_ECOLC     1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFG 251
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5s B   1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFG 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (0, 0)

(no "SCOP Domain" information available for 4B5S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B5S)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HPCH_ECOLC | B1IS70)
molecular function
    GO:0018802    2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity    Catalysis of the reaction: 2,4-dihydroxy-hept-trans-2-ene-1,7-dioate = pyruvate + succinic semialdehyde.
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0010124    phenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylacetate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPCH_ECOLC | B1IS70: 4b5t 4b5u 4b5v 4b5w 4b5x

(-) Related Entries Specified in the PDB File

4b5t CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, HPAI, IN COMPLEX WITH KETOBUTYRATE
4b5u CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, HPAI, IN COMPLEX WITH PYRUVATE AND SUCCINIC SEMIALDEHYDE
4b5v CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, HPAI, IN COMPLEX WITH 4-HYDROXYL-2- KETOHEPTANE-1,7-DIOATE
4b5w CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE R70A MUTANT, HPAI, IN COMPLEX WITH PYRUVATE
4b5x CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE (HPAI), MUTANT D42A