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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PHZG FROM PSEUDOMONAS FLUORESCENS
 
Authors :  J. F. Parsons, E. Eisenstein, J. E. Ladner
Date :  07 Jul 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 - PHENAZINE BIOSYNTHESIS PROTEIN PHZG
    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 FLUORESCENS
    Organism Taxid: 294

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:57 , SER B:78 , GLU B:79 , ILE B:80BINDING SITE FOR RESIDUE SO4 B 261
2AC2SOFTWAREARG A:126 , ASN A:129 , ARG A:178 , GLU A:180 , GLY A:181BINDING SITE FOR RESIDUE SO4 A 262
3AC3SOFTWAREARG B:126 , ASN B:129 , ARG B:178 , PRO B:179 , GLU B:180 , GLY B:181 , HOH B:698 , HOH B:699BINDING SITE FOR RESIDUE SO4 B 265
4AC4SOFTWAREHIS B:90 , ALA B:91 , GLY B:92 , ARG B:151 , GLN B:152 , GLU B:180 , GLY B:181 , HOH B:482 , HOH B:599BINDING SITE FOR RESIDUE SO4 B 266
5AC5SOFTWAREARG A:73 , ILE A:74 , VAL A:75 , VAL A:76 , SER A:88 , THR A:89 , SER A:93 , GLN A:94 , LYS A:95 , GLN A:152 , SER A:153 , HOH A:333 , HOH A:366 , HOH A:390 , HOH A:448 , HOH A:709 , LEU B:19 , TYR B:110 , GLN B:117 , TRP B:195 , ARG B:205 , HOH B:364BINDING SITE FOR RESIDUE FMN A 251
6AC6SOFTWARETYR A:110 , GLN A:117 , TRP A:195 , ARG A:205 , ARG B:73 , ILE B:74 , VAL B:75 , VAL B:76 , SER B:88 , THR B:89 , SER B:93 , GLN B:94 , LYS B:95 , GLN B:152 , SER B:153 , HOH B:305 , HOH B:410 , HOH B:446 , HOH B:452 , HOH B:465 , HOH B:495 , HOH B:609BINDING SITE FOR RESIDUE FMN B 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TY9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDOX_OXIDASEPS01064 Pyridoxamine 5'-phosphate oxidase signature.PHZG_PSEFL192-205
 		  2A:192-205
B:192-205

(-) Exons   (0, 0)

(no "Exon" information available for 1TY9)

(-) 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:202
 aligned with PHZG_PSEFL | Q51793 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:202
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
           PHZG_PSEFL    21 GTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
               SCOP domains d1ty9a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                    SCOP domains
               CATH domains 1ty9A00 A:21-222 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhh..........eeeeeeeeeeeeeeeeee..eeeeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ty9 A  21 GTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with PHZG_PSEFL | Q51793 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:207
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
           PHZG_PSEFL    16 SESLTGTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
               SCOP domains d1ty9b_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                         SCOP domains
               CATH domains 1ty9B00 B:16-222 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                               CATH domains
           Pfam domains (1) -----------------------------Pyridox_oxidase-1ty9B01 B:45-131                                                       --------------------------------------------------PNPOx_C-1ty9B03 B:182-222                 Pfam domains (1)
           Pfam domains (2) -----------------------------Pyridox_oxidase-1ty9B02 B:45-131                                                       --------------------------------------------------PNPOx_C-1ty9B04 B:182-222                 Pfam domains (2)
         Sec.struct. author ...........hhhhhhh..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee..ee...eeeeeee..hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........eeeeeeeeeeeeeeeeee..eeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ty9 B  16 SESLTGTLDAPFPEYQTLPADPMSVLHNWLERARRVGIREPRALALATADSQGRPSTRIVVISEISDAGVVFSTHAGSQKGRELLHNPWASGVLYWRETSQQIILNGQAVRLPNAKADDAWLKRPYATHPMSSVSRQSEELQDVQAMRNAARQLAELQGPLPRPEGYCVFELRLESLEFWGNGQERLHERLRYDRSDTGWNVRRLQP 222
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: FMN-binding (25)
(-)
Clan: no clan defined [family: PNPOx_C] (4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHZG_PSEFL | Q51793)
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: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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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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  PHZG_PSEFL | Q51793
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHZG_PSEFL | Q51793: 4hms 4hmt 4hmu 4hmv

(-) Related Entries Specified in the PDB File

1t9m PHZG FROM PSEUDOMONAS AERUGINOSA