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 OF PLP_THR ALDIMINE FORM OF VIBRIO CHOLERAE CQSA
 
Authors :  N. Jahan, J. A. Potter, M. A. Sheikh, C. H. Botting, S. L. Shirran, N. J. Westwood, G. L. Taylor
Date :  08 Jun 09  (Deposition) - 21 Jul 09  (Release) - 15 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxoamine-Synthases, Pyridoxal Phosphate, Cqsa, Cai-1, Transferase, Autoinducer, Quorum-Sensing, Acyltransferase, Aminotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Jahan, J. A. Potter, M. A. Sheikh, C. H. Botting, S. L. Shirran, N. J. Westwood, G. L. Taylor
Insights Into The Biosynthesis Of The Vibrio Cholerae Major Autoinducer Cai-1 From The Crystal Structure Of The Plp-Dependent Enzyme Cqsa.
J. Mol. Biol. V. 392 763 2009
PubMed-ID: 19631226  |  Reference-DOI: 10.1016/J.JMB.2009.07.042

(-) Compounds

Molecule 1 - CAI-1 AUTOINDUCER SYNTHASE
    Chains: A, B
    EC Number: 2.3.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: CHOLERAE QUORUM-SENSING AUTOINDUCER, CQSA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1PLG1Ligand/IonN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:107 , GLY A:108 , TRP A:109 , HIS A:133 , ASP A:173 , SER A:177 , ASP A:202 , SER A:204 , HIS A:205 , SER A:233 , LYS A:236 , HOH A:2287 , HOH A:2288 , PHE B:264 , SER B:265 , SER B:266BINDING SITE FOR RESIDUE PLP A 600
2AC2SOFTWAREPHE A:264 , SER A:265 , SER A:266 , HOH A:2209 , ASN B:47 , SER B:107 , GLY B:108 , TRP B:109 , HIS B:133 , ASP B:173 , SER B:177 , ASP B:202 , SER B:204 , HIS B:205 , SER B:233 , LYS B:236 , ARG B:358 , HOH B:2139 , HOH B:2346 , HOH B:2347BINDING SITE FOR RESIDUE PLG B 600
3AC3SOFTWARESER A:351 , ASN A:353 , LYS A:354 , HIS B:16BINDING SITE FOR RESIDUE SO4 A1390
4AC4SOFTWAREGLN A:291 , HIS A:292 , ARG A:295 , HOH A:2289BINDING SITE FOR RESIDUE SO4 A1391
5AC5SOFTWAREARG A:295 , GLN B:291 , HIS B:292 , ARG B:295 , HOH B:2348BINDING SITE FOR RESIDUE SO4 B1390
6AC6SOFTWARESER A:285 , ALA A:286 , ASP A:287 , ASN A:288 , ARG A:289 , HOH A:2290 , HOH A:2291BINDING SITE FOR RESIDUE SO4 A1392
7AC7SOFTWARESER B:285 , ALA B:286 , ASP B:287 , ASN B:288 , ARG B:289 , HOH B:2349 , HOH B:2350BINDING SITE FOR RESIDUE SO4 B1391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WK9)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:341 -Gly A:342
2Arg A:347 -Pro A:348
3Val A:381 -Asn A:382
4Pro B:39 -Asp B:40
5Arg B:347 -Pro B:348

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WK9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WK9)

(-) 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:382
 aligned with CQSA_VIBCH | Q9KM65 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:386
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
           CQSA_VIBCH     4 PQLPDFIQNKIDHYIENYFDINKNGKHLVLGKQASPDDIILQSNDYLALANHPLIKARLAKSLLEEQQSLFMSASFLQNDYDKPMIEKRLAKFTGFDECLLSQSGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANAQAHPFMHNNCDHLRMLIQRHGPGIIVVDSIYSTLGTIAPLAELVNISKEFGCALLVDESHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTFAYRAGAIWCNNEVNRCVPFISYPAIFSSTLLPYEAAGLETTLEIIESADNRRQHLDRMARKLRIGLSQLGLTIRSESQIIGLETGDERNTEKVRDYLESNGVFGSVFCRPATSKNKNIIRLSLNSDVNDEQIAKIIEVCSDAVNYGDFYFR 389
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.---.............-..............hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhh....eeeee...hhhhhh.......eeeee...hhhhhhhhhhhh....eeee..........hhhhhhhhhhhh...eeee....................hhhhh.eee.............eee..hhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhhhhhh.....ee..........eeeee.....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk9 A   4 PQLPDFIQNKIDHYIENYFD---NGKHLVLGKQASP-DIILQSNDYLALANHPLIKARLAKSLLEEQQSLFMSASFLQNDYDKPMIEKRLAKFTGFDECLLSQSGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANAQAHPFMHNNCDHLRMLIQRHGPGIIVVDSIYSTLGTIAPLAELVNISKEFGCALLVDESHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTFAYRAGAIWCNNEVNRCVPFISYPAIFSSTLLPYEAAGLETTLEIIESADNRRQHLDRMARKLRIGLSQLGLTIRSESQIIGLETGDERNTEKVRDYLESNGVFGSVFCRPATSKNKNIIRLSLNSDVNDEQIAKIIEVCSDAVNYGDFYFR 389
                                    13        23   |    33     | |43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
                                              23  27          39 |                                                                                                                                                                                                                                                                                                                                                            
                                                                41                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:380
 aligned with CQSA_VIBCH | Q9KM65 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:386
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
           CQSA_VIBCH     4 PQLPDFIQNKIDHYIENYFDINKNGKHLVLGKQASPDDIILQSNDYLALANHPLIKARLAKSLLEEQQSLFMSASFLQNDYDKPMIEKRLAKFTGFDECLLSQSGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANAQAHPFMHNNCDHLRMLIQRHGPGIIVVDSIYSTLGTIAPLAELVNISKEFGCALLVDESHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTFAYRAGAIWCNNEVNRCVPFISYPAIFSSTLLPYEAAGLETTLEIIESADNRRQHLDRMARKLRIGLSQLGLTIRSESQIIGLETGDERNTEKVRDYLESNGVFGSVFCRPATSKNKNIIRLSLNSDVNDEQIAKIIEVCSDAVNYGDFYFR 389
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------Aminotran_1_2-2wk9B01 B:39-376                                                                                                                                                                                                                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Aminotran_1_2-2wk9B02 B:39-376                                                                                                                                                                                                                                                                                                                    ------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhh................................hhhhhhhhhhhhh.------.hhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhh....eeeee...hhhhhh.......eeeee...hhhhhhhhhhhh....eeee..........hhhhhhhhhhhh...eeee....................hhhhh.eee.............eee..hhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeee..hhhhhhhhhhhhhhh.....ee..........eeeee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk9 B   4 PQLPDFIQNKIDHYIENYFDINKNGKHLVLGKQASPDDIILQSNDYLALANHPLIKARLAKSLLE------MSASFLQNDYDKPMIEKRLAKFTGFDECLLSQSGWNANVGLLQTICQPNTNVYIDFFAHMSLWEGARYANAQAHPFMHNNCDHLRMLIQRHGPGIIVVDSIYSTLGTIAPLAELVNISKEFGCALLVDESHSLGTHGPNGAGLLAELGLTREVHFMTASLAKTFAYRAGAIWCNNEVNRCVPFISYPAIFSSTLLPYEAAGLETTLEIIESADNRRQHLDRMARKLRIGLSQLGLTIRSESQIIGLETGDERNTEKVRDYLESNGVFGSVFCRPATSKNKNIIRLSLNSDVNDEQIAKIIEVCSDAVNYGDFYFR 389
                                    13        23        33        43        53        63    |    - |      83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
                                                                                           68     75
   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  (0, 0)

(no "SCOP Domain" information available for 2WK9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WK9)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CQSA_VIBCH | Q9KM65)
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:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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.

 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
    PLG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:347 - Pro A:348   [ RasMol ]  
    Arg B:347 - Pro B:348   [ RasMol ]  
    Phe A:341 - Gly A:342   [ RasMol ]  
    Pro B:39 - Asp B:40   [ RasMol ]  
    Val A:381 - Asn A:382   [ RasMol ]  
 

(-) 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
  2wk9
    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
  CQSA_VIBCH | Q9KM65
    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)
  2.3.-.-
    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
  CQSA_VIBCH | Q9KM65
    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
        CQSA_VIBCH | Q9KM65: 2wk7 2wk8 2wka 3hqt 3kki

(-) Related Entries Specified in the PDB File

2wk7 STRUCTURE OF APO FORM OF VIBRIO CHOLERAE CQSA
2wk8 STRUCTURE OF HOLO FORM OF VIBRIO CHOLERAE CQSA
2wka STRUCTURE OF PLP_THR_DECANOYL-COA ALDIMINE FORM OF VIBRIO CHOLERAE CQSA