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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-AMINO-4-DEOXYCHORISMATE LYASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  P. E. F. O'Rourke, T. C. Eadsforth, P. K. Fyfe, S. M. Shepard, M. Agacan, W. N. Hunter
Date :  10 Jan 11  (Deposition) - 19 Jan 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Para-Aminobenzoic Acid, Folate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. E. F. O'Rourke, T. C. Eadsforth, P. K. Fyfe, S. M. Shepherd, W. N. Hunter
Pseudomonas Aeruginosa 4-Amino-4-Deoxychorismate Lyase: Spatial Conservation Of An Active Site Tyrosine And Classification Of Two Types Of Enzyme.
Plos One V. 6 24158 2011
PubMed-ID: 21935381  |  Reference-DOI: 10.1371/JOURNAL.PONE.0024158

(-) Compounds

Molecule 1 - 4-AMINO-4-DEOXYCHORISMATE LYASE
    Atcc: 47085
    Chains: A, B
    EC Number: 4.1.3.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)GOLD
    Expression System Taxid: 469008
    Expression System Vector: PET15BTEV
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Other Details: LYSINE 140 IS COVALENTLY LINKED TO A PYRIDOXAL PHOSPHATE COFACTOR
    Strain: PAO1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 20)

Asymmetric/Biological Unit (7, 20)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PG45Ligand/IonTETRAETHYLENE GLYCOL
6PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
7SO42Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:46 , LYS A:140 , GLU A:173 , VAL A:175 , SER A:177 , ASN A:178 , VAL A:197 , GLY A:199 , VAL A:200 , MET A:201 , ASN A:236 , SER A:237 , HOH A:2231 , TYR B:92BINDING SITE FOR RESIDUE PLP A1140
02AC2SOFTWAREGLU A:49 , ARG A:53 , HOH A:2232BINDING SITE FOR RESIDUE PG4 A1272
03AC3SOFTWAREARG A:127 , THR A:128 , LEU A:149 , GLU A:153 , HOH A:2112 , HOH A:2233 , LEU B:135BINDING SITE FOR RESIDUE PG4 A1273
04AC4SOFTWAREALA A:34 , GLY A:75 , GLU A:207 , GLU A:210 , LEU A:216 , ILE A:218BINDING SITE FOR RESIDUE PG4 A1274
05AC5SOFTWAREARG A:102BINDING SITE FOR RESIDUE CL A1275
06AC6SOFTWAREARG A:122BINDING SITE FOR RESIDUE CL A1276
07AC7SOFTWARELEU A:192 , ARG A:202 , ILE A:218 , PEG A:1280 , HOH A:2234 , HOH A:2235 , HOH A:2236BINDING SITE FOR RESIDUE SO4 A1277
08AC8SOFTWAREARG A:194 , ARG A:208 , ASP A:268 , HOH A:2120 , HOH A:2237BINDING SITE FOR RESIDUE EDO A1278
09AC9SOFTWAREPRO A:215 , HOH A:2238 , ALA B:224BINDING SITE FOR RESIDUE EDO A1279
10BC1SOFTWAREALA A:203 , GLU A:207 , ILE A:218 , SO4 A:1277 , HOH A:2014BINDING SITE FOR RESIDUE PEG A1280
11BC2SOFTWAREARG A:90 , GLY A:91 , TYR A:92 , ALA A:93 , ARG B:151 , PHE B:176BINDING SITE FOR RESIDUE GOL A1281
12BC3SOFTWAREHIS A:168 , HIS B:168BINDING SITE FOR RESIDUE CL A1282
13BC4SOFTWARETYR A:92 , ARG B:46 , LYS B:140 , GLN B:147 , GLU B:173 , VAL B:175 , SER B:177 , ASN B:178 , VAL B:197 , GLY B:199 , VAL B:200 , MET B:201 , ASN B:236 , SER B:237 , HOH B:2225BINDING SITE FOR RESIDUE PLP B1140
14BC5SOFTWAREGLU B:49 , ARG B:53 , GLY B:138 , ASP B:156 , ALA B:198 , PEG B:1277 , HOH B:2226 , HOH B:2232 , HOH B:2233BINDING SITE FOR RESIDUE PG4 B1272
15BC6SOFTWAREARG A:53 , LEU A:54 , ALA A:55 , PRO A:94 , LEU A:135 , THR B:128 , LEU B:149 , ALA B:152 , GLU B:153 , HOH B:2227 , HOH B:2229 , HOH B:2230BINDING SITE FOR RESIDUE PG4 B1273
16BC7SOFTWAREGLY B:120 , ARG B:245 , HOH B:2231BINDING SITE FOR RESIDUE PEG B1274
17BC8SOFTWARELEU B:192 , ARG B:202 , ILE B:218 , HOH B:2232 , HOH B:2233BINDING SITE FOR RESIDUE SO4 B1275
18BC9SOFTWAREGLU B:48 , CYS B:51 , ILE B:56 , LEU B:58BINDING SITE FOR RESIDUE EDO B1276
19CC1SOFTWAREHIS B:159 , PG4 B:1272 , HOH B:2234BINDING SITE FOR RESIDUE PEG B1277
20CC2SOFTWAREARG A:151 , PHE A:176 , ARG B:90 , GLY B:91 , TYR B:92 , ALA B:93 , HOH B:2235BINDING SITE FOR RESIDUE GOL B1278

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y4R)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4R)

(-) 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:270
 aligned with Q9HZN6_PSEAE | Q9HZN6 from UniProtKB/TrEMBL  Length:271

    Alignment length:270
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
         Q9HZN6_PSEAE     2 LDWVDGRPAAELSVRDRGLAYGDGLFETLAVRAGTPRLLERHLARLEEGCRRLAIPLDTAALRQELLAFCAALGDGVAKLIVTRGEGLRGYAPPAEASPRRILSGSPRPAYPERHWQQGVRLFACRTRLAEQPLLAGLKHLNRLEQVLARAEWSDAGHAEGLMLDVHERVVEGVFSNLLLVLDGTLVAPDLRRCGVAGVMRAELLERAEGIGVPLAIRDVSMAELATADEVFLCNSQFGIWPVRALDEHVWPVGELTRKLQDQLRDDLDF 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..ee..eee..hhhhhhh.eeeeeeeee..ee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeeeee................eeeeeee.....hhhhhhh.eeeee..................hhhhhhhhh........eeeee.....eeee...eeeeee..eeeee........hhhhhhhhhhhhhh...eeee..hhhhhhh...........eeeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4r A   2 LDWVDGRPAAELSVRDRGLAYGDGLFETLAVRAGTPRLLERHLARLEEGCRRLAIPLDTAALRQELLAFCAALGDGVAKLIVTRGEGLRGYAPPAEASPRRILSGSPRPAYPERHWQQGVRLFACRTRLAEQPLLAGLKHLNRLEQVLARAEWSDAGHAEGLMLDVHERVVEGVFSNLLLVLDGTLVAPDLRRCGVAGVMRAELLERAEGIGVPLAIRDVSMAELATADEVFLCNSQFGIWPVRALDEHVWPVGELTRKLQDQLRDDLDF 271
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with Q9HZN6_PSEAE | Q9HZN6 from UniProtKB/TrEMBL  Length:271

    Alignment length:270
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
         Q9HZN6_PSEAE     2 LDWVDGRPAAELSVRDRGLAYGDGLFETLAVRAGTPRLLERHLARLEEGCRRLAIPLDTAALRQELLAFCAALGDGVAKLIVTRGEGLRGYAPPAEASPRRILSGSPRPAYPERHWQQGVRLFACRTRLAEQPLLAGLKHLNRLEQVLARAEWSDAGHAEGLMLDVHERVVEGVFSNLLLVLDGTLVAPDLRRCGVAGVMRAELLERAEGIGVPLAIRDVSMAELATADEVFLCNSQFGIWPVRALDEHVWPVGELTRKLQDQLRDDLDF 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------Aminotran_4-2y4rB01 B:38-265                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) ------------------------------------Aminotran_4-2y4rB02 B:38-265                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author .eee..ee..eee..hhhhhhh.eeeeeeeee..ee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeeee................eeeeeee.....hhhhhhhheeeee..................hhhhhhhhh........eeeee.....eeee...eeeee....eeee........hhhhhhhhhhhhhh...eeee..hhhhhhh...........eeeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4r B   2 LDWVDGRPAAELSVRDRGLAYGDGLFETLAVRAGTPRLLERHLARLEEGCRRLAIPLDTAALRQELLAFCAALGDGVAKLIVTRGEGLRGYAPPAEASPRRILSGSPRPAYPERHWQQGVRLFACRTRLAEQPLLAGLKHLNRLEQVLARAEWSDAGHAEGLMLDVHERVVEGVFSNLLLVLDGTLVAPDLRRCGVAGVMRAELLERAEGIGVPLAIRDVSMAELATADEVFLCNSQFGIWPVRALDEHVWPVGELTRKLQDQLRDDLDF 271
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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 2Y4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4R)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Aminotran_4] (8)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9HZN6_PSEAE | Q9HZN6)
molecular function
    GO:0008696    4-amino-4-deoxychorismate lyase activity    Catalysis of the reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + H(+) + pyruvate.
    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:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0046656    folic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
    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.

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  2y4r
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