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(-) Description

Title :  CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE (HPAI), MUTANT D42A
 
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 :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Lyase, Catalytic Mechanism (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 Plasmid: PT7-7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO48Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2PO424Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:26 , GLU B:44 , HIS B:45 , ASP B:84 , VAL B:85 , ALA B:123 , ARG B:124 , HOH B:2065 , HOH B:2104 , HOH B:2106BINDING SITE FOR RESIDUE PO4 B 1254
02AC2SOFTWARESER A:24 , TYR A:26 , HOH A:2071 , LEU B:22 , SER B:23 , SER B:24 , HIS B:45 , HOH B:2385BINDING SITE FOR RESIDUE PO4 B 1255
03AC3SOFTWAREHIS A:45 , ASP A:84 , VAL A:85 , ALA A:123 , ARG A:124 , HOH A:2064 , HOH A:2212 , HOH A:2291 , TYR B:26BINDING SITE FOR RESIDUE PO4 A 1252
04AC4SOFTWARELEU A:22 , SER A:23 , SER A:24 , HIS A:45 , HOH A:2117 , HOH A:2446 , SER B:24 , TYR B:26 , HOH B:2385BINDING SITE FOR RESIDUE PO4 A 1253
05AC5SOFTWARELYS A:6 , ARG A:109 , GLU A:164 , ASP A:167 , HOH A:2319 , HOH A:2345BINDING SITE FOR RESIDUE PO4 A 1254
06AC6SOFTWARELYS B:6 , ARG B:109 , GLU B:164 , ASP B:167BINDING SITE FOR RESIDUE PO4 B 1256
07AC7SOFTWAREARG B:70 , LYS B:80 , GLY B:117 , GLY B:119 , GLU B:149 , ASP B:175 , HOH B:2148 , HOH B:2236 , HOH B:2386BINDING SITE FOR RESIDUE PO4 B 1257
08AC8SOFTWAREARG A:70 , LYS A:80 , GLY A:117 , GLY A:119 , GLU A:149 , ASP A:175 , HOH A:2447 , HOH A:2448 , HOH A:2449BINDING SITE FOR RESIDUE PO4 A 1255
09AC9SOFTWAREARG A:127 , HOH A:2294 , PRO B:62 , TYR B:63BINDING SITE FOR RESIDUE GOL B 1258
10BC1SOFTWAREPRO A:62 , TYR A:63 , HOH A:2081 , ARG B:127BINDING SITE FOR RESIDUE GOL A 1256

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5X)

(-) 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 4B5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5X)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5X)

(-) 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....eeee.......hhhhhhhhhhhhh....eeee.....hhhhhhhhhhh...eeee....hhhhhhhhhhh...............hhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhh....eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5x A   1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIAGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFG 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:253
 aligned with HPCH_ECOLC | B1IS70 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:253
                                    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 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQ 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeee...hhhhhhhhhh....eeee......hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..eeee....hhhhhhhhhhhh..............hhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5x B   1 MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIAGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQ 253
                                    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)
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  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 4B5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B5X)

(-) 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: 4b5s 4b5t 4b5u 4b5v 4b5w

(-) Related Entries Specified in the PDB File

2v5j APO CLASS II ALDOLASE HPCH
2v5k CLASS II ALDOLASE HPCH - MAGNESIUM - OXAMATE COMPLEX
4b5s CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDOLASE, HPAI, IN COMPLEX WITH PYRUVATE
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