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(-) Description

Title :  STRUCTURE AND FUNCTION OF THE PHENAZINE BIOSYNTHETIC PROTEIN PHZF FROM PSEUDOMONAS FLUORESCENS
 
Authors :  W. Blankenfeldt, A. P. Kuzin, T. Skarina, Y. Korniyenko, L. Tong, P. Bay P. Janning, L. S. Thomashow, D. V. Mavrodi
Date :  26 Oct 04  (Deposition) - 09 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phenazine Biosynthesis, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Blankenfeldt, A. P. Kuzin, T. Skarina, Y. Korniyenko, L. Tong, P. Bayer, P. Janning, L. S. Thomashow, D. V. Mavrodi
Structure And Function Of The Phenazine Biosynthetic Protei Phzf From Pseudomonas Fluorescens
Proc. Natl. Acad. Sci. Usa V. 101 16431 2004
PubMed-ID: 15545603  |  Reference-DOI: 10.1073/PNAS.0407371101

(-) Compounds

Molecule 1 - PHENAZINE BIOSYNTHESIS PROTEIN PHZF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HHA2Ligand/Ion(2S,3S)-TRANS-2,3-DIHYDRO-3-HYDROXYANTHRANILIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:45 , LEU A:69 , ALA A:72 , GLY A:73 , HIS A:74 , PRO A:75 , MET A:198 , ASP A:208 , ALA A:210 , THR A:211 , GLY A:212 , SER A:213 , HOH A:1019BINDING SITE FOR RESIDUE HHA A 1001
2AC2SOFTWAREGLU B:45 , LEU B:69 , ALA B:72 , GLY B:73 , HIS B:74 , PRO B:75 , MET B:198 , ASP B:208 , ALA B:210 , THR B:211 , GLY B:212 , SER B:213 , HOH B:1017BINDING SITE FOR RESIDUE HHA B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XUA)

(-) 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:278
 aligned with PHZF_PSEFL | Q51792 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:278
                                    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       260       270        
           PHZF_PSEFL     1 MHNYVIIDAFASVPLEGNPVAVFFDADDLPPAQMQRIAREMNLSESTFVLKPRNGGDALIRIFTPVNELPFAGHPLLGTAIALGAHTDNHRLYLETQMGTIAFELERQNGSVIAASMDQPIPTWTALGRDAELLKALGISDSTFPIEIYHNGPRHVFVGLPSIDALSALHPDHRALSNFHDMAINCFAGAGRRWRSRMFSPAYGVVEDAATGSAAGPLAIHLARHGQIEFGQPVEILQGVEIGRPSLMFAKAEGRAEQLTRVEVSGNGVTFGRGTIVL 278
               SCOP domains d1xuaa1 A:1-128 Phenazine biosynthesis protein PhzF                                                                             d1xuaa2 A:129-278 Phenazine biosynthesis protein PhzF                                                                                                  SCOP domains
               CATH domains 1xuaA01 A:1-119,A:268-278 Diaminopimelate Epimerase; Chain A, domain 1                                                 1xuaA02 A:120-267 Diaminopimelate Epimerase; Chain A, domain 1                                                                                      1xuaA01     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeee......hhhhhhhhhhhhh...eeeee.......eeeeee....ee..hhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee..eeeeeeee....eeee..hhhhhhhhhh........eeee...eeeeee..hhhhhhhh..hhhhhh.....eeeeeeee..eeeeeeeehhhheeee..hhhhhhhhhhhhhhh........eeeee.......eeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xua A   1 MHNYVIIDAFASVPLEGNPVAVFFDADDLPPAQMQRIAREMNLSESTFVLKPRNGGDALIRIFTPVNELPFAGHPLLGTAIALGAHTDNHRLYLETQMGTIAFELERQNGSVIAASMDQPIPTWTALGRDAELLKALGISDSTFPIEIYHNGPRHVFVGLPSIDALSALHPDHRALSNFHDMAINCFAGAGRRWRSRMFSPAYGVVEDAATGSAAGPLAIHLARHGQIEFGQPVEILQGVEIGRPSLMFAKAEGRAEQLTRVEVSGNGVTFGRGTIVL 278
                                    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       260       270        


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with PHZF_PSEFL | Q51792 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:279
                             1                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269         
           PHZF_PSEFL     - -MHNYVIIDAFASVPLEGNPVAVFFDADDLPPAQMQRIAREMNLSESTFVLKPRNGGDALIRIFTPVNELPFAGHPLLGTAIALGAHTDNHRLYLETQMGTIAFELERQNGSVIAASMDQPIPTWTALGRDAELLKALGISDSTFPIEIYHNGPRHVFVGLPSIDALSALHPDHRALSNFHDMAINCFAGAGRRWRSRMFSPAYGVVEDAATGSAAGPLAIHLARHGQIEFGQPVEILQGVEIGRPSLMFAKAEGRAEQLTRVEVSGNGVTFGRGTIVL 278
               SCOP domains -d1xuab1 B:1-128 Phenazine biosynthesis protein PhzF                                                                             d1xuab2 B:129-278 Phenazine biosynthesis protein PhzF                                                                                                  SCOP domains
               CATH domains 1xuaB01 B:0-119,B:268-278 Diaminopimelate Epimerase; Chain A, domain 1                                                  1xuaB02 B:120-267 Diaminopimelate Epimerase; Chain A, domain 1                                                                                      1xuaB01     CATH domains
           Pfam domains (1) -------PhzC-PhzF-1xuaB01 B:7-274                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) -------PhzC-PhzF-1xuaB02 B:7-274                                                                                                                                                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author ..eeeeeeee........eeeeee.hhhhhhhhhhhhhhhhhh..eeeeee.......eeeeee....ee..hhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee..eeeeeeee....eeee..hhhhhhhhhh........eeee...eeeeee..hhhhhhhh..hhhhhh.....eeeeeeee..eeeeeeeehhhheeee..hhhhhhhhhhhhhhh........eeeee.......eeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xua B   0 HMHNYVIIDAFASVPLEGNPVAVFFDADDLPPAQMQRIAREMNLSESTFVLKPRNGGDALIRIFTPVNELPFAGHPLLGTAIALGAHTDNHRLYLETQMGTIAFELERQNGSVIAASMDQPIPTWTALGRDAELLKALGISDSTFPIEIYHNGPRHVFVGLPSIDALSALHPDHRALSNFHDMAINCFAGAGRRWRSRMFSPAYGVVEDAATGSAAGPLAIHLARHGQIEFGQPVEILQGVEIGRPSLMFAKAEGRAEQLTRVEVSGNGVTFGRGTIVL 278
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DAP_epimerase (14)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHZF_PSEFL | Q51792)
molecular function
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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.

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  1xua
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  PHZF_PSEFL | Q51792
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHZF_PSEFL | Q51792: 1t6k 1u1v 1u1w 1u1x 1xub 5iwe

(-) Related Entries Specified in the PDB File

1u1v WT SULFATE COMPLEX
1u1w WT 3-HYDROXYANTHRANILIC ACID COMPLEX
1u1x WT DHHA COMPLEX