Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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 :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phenazine Biosynthesis, Acid/Base Catalysis, Closed Form, Substrate Complex, Isomerase, 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, B
    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

  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 , 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:407BINDING SITE FOR RESIDUE HHA A 401
2AC2SOFTWAREGLU B:45 , 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:417BINDING SITE FOR RESIDUE HHA B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U1X)

(-) Exons   (0, 0)

(no "Exon" information available for 1U1X)

(-) 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 d1u1xa1 A:1-128 Phenazine biosynthesis protein PhzF                                                                             d1u1xa2 A:129-278 Phenazine biosynthesis protein PhzF                                                                                                  SCOP domains
               CATH domains 1u1xA01 A:1-119,A:268-278 Diaminopimelate Epimerase; Chain A, domain 1                                                 1u1xA02 A:120-267 Diaminopimelate Epimerase; Chain A, domain 1                                                                                      1u1xA01     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
                 1u1x 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 -d1u1xb1 B:1-128 Phenazine biosynthesis protein PhzF                                                                             d1u1xb2 B:129-278 Phenazine biosynthesis protein PhzF                                                                                                  SCOP domains
               CATH domains 1u1xB01 B:0-119,B:268-278 Diaminopimelate Epimerase; Chain A, domain 1                                                  1u1xB02 B:120-267 Diaminopimelate Epimerase; Chain A, domain 1                                                                                      1u1xB01     CATH domains
           Pfam domains (1) -------PhzC-PhzF-1u1xB01 B:7-274                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) -------PhzC-PhzF-1u1xB02 B:7-274                                                                                                                                                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author ..eeeeeeee........eeeeee......hhhhhhhhhhhhh...eeeee.......eeeeee....ee..hhhhhhhhhhhhhh.....eeeeee..eeeeeeeee....eeeeeee....eeee..hhhhhhhhhh........eeee...eeeeee..hhhhhhhh..hhhhhhh....eeeeeeee..eeeeeeeehhhheeee..hhhhhhhhhhhhhhh........eeeee.......eeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1x 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    HHA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1u1x)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1u1x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PHZF_PSEFL | Q51792
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PHZF_PSEFL | Q51792
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1bwz DIAMINOPIMELATE EPIMERASE DAPF
1s7j PHENAZINE BIOSYNTHESIS PROTEIN E. FAECALIS
1sdj YDDE E. COLI
1u1v
1u1w