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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PHZG FROM PSEUDOMONAS AERUGINOSA
 
Authors :  J. F. Parsons, E. Eisenstein, J. E. Ladner
Date :  18 May 04  (Deposition) - 02 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phenazine, Phzg, Chorismate, Pseudomonas, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. F. Parsons, K. Calabrese, E. Eisenstein, J. E. Ladner
Structure Of The Phenazine Biosynthesis Enzyme Phzg.
Acta Crystallogr. , Sect. D V. 60 2110 2004
PubMed-ID: 15502343  |  Reference-DOI: 10.1107/S0907444904022474
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHZG
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , GLN A:59 , ARG A:61 , HOH B:748BINDING SITE FOR RESIDUE SO4 A 351
2AC2SOFTWAREARG A:118 , ARG A:170 , PRO A:172 , GLY A:173BINDING SITE FOR RESIDUE SO4 A 352
3AC3SOFTWAREARG B:118 , ARG B:170 , PRO B:172 , GLY B:173 , HOH B:721BINDING SITE FOR RESIDUE SO4 B 353
4AC4SOFTWAREARG A:41 , ARG A:42 , PRO B:95 , TRP B:96 , ARG B:115BINDING SITE FOR RESIDUE SO4 B 354
5AC5SOFTWAREARG A:65 , ILE A:66 , VAL A:67 , VAL A:68 , ALA A:80 , THR A:81 , SER A:85 , GLN A:86 , LYS A:87 , GLN A:144 , SER A:145 , HOH A:420 , HOH A:421 , HOH A:427 , HOH A:431 , HOH A:487 , TYR B:102 , GLN B:109 , TRP B:187 , ARG B:197 , HOH B:405BINDING SITE FOR RESIDUE FMN A 250
6AC6SOFTWARETYR A:102 , GLN A:109 , TRP A:187 , ARG A:197 , HOH A:403 , HOH A:670 , ARG B:65 , ILE B:66 , VAL B:67 , VAL B:68 , ALA B:80 , THR B:81 , SER B:85 , GLN B:86 , LYS B:87 , GLN B:144 , SER B:145 , HOH B:408 , HOH B:430 , HOH B:444 , HOH B:446BINDING SITE FOR RESIDUE FMN B 350
7AC7SOFTWARETYR A:102 , ARG A:104 , HOH A:452 , TYR B:102 , ARG B:104 , HOH B:552BINDING SITE FOR RESIDUE ACY B 301
8AC8SOFTWAREARG A:46 , GLU A:105 , HOH A:402 , GLU B:105 , HOH B:412BINDING SITE FOR RESIDUE ACY B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T9M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T9M)

(-) Exons   (0, 0)

(no "Exon" information available for 1T9M)

(-) 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:204
 aligned with O69755_PSEAI | O69755 from UniProtKB/TrEMBL  Length:214

    Alignment length:204
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
         O69755_PSEAI    11 LTGTIEAPFPEFEAPPANPMEVLRNWLERARRYGVREPRALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQWLSRPYQTHPMSIASRQSETLADIHALRAEARRLAETDGPLPRPPGYCLFELCLESVEFWGNGTERLHERLRYDRDEGGWKHRYLQP 214
               SCOP domains d1t9ma_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                      SCOP domains
               CATH domains 1t9mA00 A:11-214 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...........eeeeeeeeeeeeeeeeee..eeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t9m A  11 LTGTIEAPFPEFEAPPANPMEVLRNWLERARRYGVREPRALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQWLSRPYQTHPMSIASRQSETLADIHALRAEARRLAETDGPLPRPPGYCLFELCLESVEFWGNGTERLHERLRYDRDEGGWKHRYLQP 214
                                    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:204
 aligned with O69755_PSEAI | O69755 from UniProtKB/TrEMBL  Length:214

    Alignment length:204
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
         O69755_PSEAI    11 LTGTIEAPFPEFEAPPANPMEVLRNWLERARRYGVREPRALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQWLSRPYQTHPMSIASRQSETLADIHALRAEARRLAETDGPLPRPPGYCLFELCLESVEFWGNGTERLHERLRYDRDEGGWKHRYLQP 214
               SCOP domains d1t9mb_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                      SCOP domains
               CATH domains 1t9mB00 B:11-214 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........eeeeeeeeeeeeeee.......eeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t9m B  11 LTGTIEAPFPEFEAPPANPMEVLRNWLERARRYGVREPRALALATVDGQGRPSTRIVVIAELGERGVVFATHADSQKGRELAQNPWASGVLYWRESSQQIILNGRAERLPDERADAQWLSRPYQTHPMSIASRQSETLADIHALRAEARRLAETDGPLPRPPGYCLFELCLESVEFWGNGTERLHERLRYDRDEGGWKHRYLQP 214
                                    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)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1T9M)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O69755_PSEAI | O69755)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016638    oxidoreductase activity, acting on the CH-NH2 group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0002047    phenazine biosynthetic process    The chemical reactions and pathways resulting in the formation of a phenazine antibiotic, a polycyclic pyrazine with two nitrogen atoms in the ring.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0008615    pyridoxine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1np9 PHZD IS ANOTHER ENZYME IN THE PHENAZINE CHORISMATE PATHWAY
1t6k PHZF IS ANOTHER ENZYME IN THE PHENAZINE CHORISMATE PATHWAY