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(-) Description

Title :  STRUCTURE AND FUNCTION OF PHENAZINE-BIOSYNTHESIS PROTEIN PHZF FROM PSEUDOMONAS FLUORESCENS 2-79
 
Authors :  W. Blankenfeldt, A. P. Kuzin, T. Skarina, Y. Korniyenko, L. Tong, P. Bay P. Janning, L. S. Thomashow, D. V. Mavrodi
Date :  16 Jul 04  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phenazine Biosynthesis, Isomerase, Open Form, Acid/Base Catalysis, Lyase (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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA PLYS S
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHZF
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:72 , GLY A:73 , HIS A:74 , PRO A:75 , ALA A:210 , THR A:211 , GLY A:212 , SER A:213 , HOH A:531 , HOH A:716BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREHIS A:90 , ARG A:129 , ARG A:154 , MSE A:182BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARELEU A:50 , LYS A:51 , LEU A:83 , HOH A:546BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U1V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U1V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U1V)

(-) Exons   (0, 0)

(no "Exon" information available for 1U1V)

(-) 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: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 d1u1va1 A:1-128 Phenazine biosynthesis protein PhzF                                                                             d1u1va2 A:129-278 Phenazine biosynthesis protein PhzF                                                                                                  SCOP domains
               CATH domains -1u1vA01 A:2-119,A:268-278 Diaminopimelate Epimerase; Chain A, domain 1                                                1u1vA02 A:120-267 Diaminopimelate Epimerase; Chain A, domain 1                                                                                      1u1vA01     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeee.hhhhhhhhhhhhhhhhhh...eeeee.......eeeeee....ee..hhhhhhhhhhhhhhhh...eeeeee..eeeeeeeeee..eeeeeeee....eeee..hhhhhhhhhh........eeee...eeeeee..hhhhhhhh..hhhhhh.....eeeeeeee..eeeeeeee....eeee..hhhhhhhhhhhhhhh........eeeee.......eeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1v 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        
                            |                               34-MSE 41-MSE                                                   98-MSE            117-MSE                                                          182-MSE         198-MSE                                           248-MSE                          
                            1-MSE
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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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U1V)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  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 1u1w 1u1x 1xua 1xub 5iwe

(-) Related Entries Specified in the PDB File

1bwz DIAMINOPIMELATE EPIMERASE
1s7j PHENAZINE-BIOSYNTHESIS PROTEIN FROM E.FAECALIS
1sdj YDDE E.COLI
1u1w
1u1x