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(-) Description

Title :  CRYSTAL STRUCTURE OF MG2+ AND BEF3- BOUND CHEY IN COMPLEX WITH CHEZ 200-214 SOLVED FROM A P2(1)2(1)2 CRYSTAL GROWN IN MES (PH 6.0)
 
Authors :  J. Guhaniyogi, V. L. Robinson, A. M. Stock
Date :  09 Jan 06  (Deposition) - 23 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chemotaxis; Bef(3)(-)-Bound Chey; Chey-Chez Peptide Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Guhaniyogi, V. L. Robinson, A. M. Stock
Crystal Structures Of Beryllium Fluoride-Free And Beryllium Fluoride-Bound Chey In Complex With The Conserved C-Termina Peptide Of Chez Reveal Dual Binding Modes Specific To Chey Conformation
J. Mol. Biol. V. 359 624 2006
PubMed-ID: 16674976  |  Reference-DOI: 10.1016/J.JMB.2006.03.050

(-) Compounds

Molecule 1 - CHEMOTAXIS PROTEIN CHEY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CHEY
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
 
Molecule 2 - C-TERMINAL 15-MER FROM CHEMOTAXIS PROTEIN CHEZ
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 200-214
    Other Details: THIS SEQUENCE CORRESPONDS TO THE C-TERMINAL 15 RESIDUES OF THE CHEZ PROTEIN OCCURRING NATURALLY IN SALMONELLA ENTERICA SEROVAR TYPHUMURIUM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , ASP A:57 , ASN A:59 , BEF A:501 , HOH A:9003 , HOH A:9035BINDING SITE FOR RESIDUE MG A 9001
2AC2SOFTWAREASP A:57 , TRP A:58 , ASN A:59 , THR A:87 , ALA A:88 , LYS A:109 , MG A:9001 , HOH A:9003 , HOH A:9009 , HOH A:9035BINDING SITE FOR RESIDUE BEF A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:109 -Pro A:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.CHEY_SALTY7-124  1A:7-124

(-) Exons   (0, 0)

(no "Exon" information available for 2FMK)

(-) 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:128
 aligned with CHEY_SALTY | P0A2D5 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
           CHEY_SALTY     2 ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
               SCOP domains d2fmka_ A: CheY protein                                                                                                          SCOP domains
               CATH domains 2fmkA00 A:2-129  [code=3.40.50.2300, no name defined]                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...eeeeee.......hhhhhhhhhhh........eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RESPONSE_REGULATORY  PDB: A:7-124 UniProt: 7-124                                                                      ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmk A   2 ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain B from PDB  Type:PROTEIN  Length:16
 aligned with CHEZ_SALTY | P07800 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:16
                                   208      
           CHEZ_SALTY   199 VASQDQVDDLLDSLGF 214
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2fmk B 199 xASQDQVDDLLDSLGF 214
                            |      208      
                          199-ACE           


Chain B from PDB  Type:PROTEIN  Length:16
 aligned with Q57N83_SALCH | Q57N83 from UniProtKB/TrEMBL  Length:188

    Alignment length:16
                                   182      
         Q57N83_SALCH   173 VASQDQVDDLLDSLGF 188
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2fmk B 199 xASQDQVDDLLDSLGF 214
                            |      208      
                          199-ACE
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FMK)

(-) Gene Ontology  (11, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHEY_SALTY | P0A2D5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0097588    archaeal or bacterial-type flagellum-dependent cell motility    Cell motility due to movement of bacterial- or archaeal-type flagella.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (CHEZ_SALTY | P07800)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
biological process
    GO:0097588    archaeal or bacterial-type flagellum-dependent cell motility    Cell motility due to movement of bacterial- or archaeal-type flagella.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0050920    regulation of chemotaxis    Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
cellular component
    GO:0009288    bacterial-type flagellum    A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (Q57N83_SALCH | Q57N83)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
biological process
    GO:0097588    archaeal or bacterial-type flagellum-dependent cell motility    Cell motility due to movement of bacterial- or archaeal-type flagella.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0050920    regulation of chemotaxis    Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
cellular component
    GO:0009288    bacterial-type flagellum    A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHEY_SALTY | P0A2D5: 2che 2chf 2chy 2fka 2flk 2flw 2fmf 2fmh 2fmi 2pl9 2pmc
        CHEZ_SALTY | P07800: 2fka 2flk 2flw 2fmf 2fmh 2fmi 2pl9 2pmc

(-) Related Entries Specified in the PDB File

2fka THE MG2+ AND BEF3--BOUND CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP BUT SOLVED FROM CRYSTALS GROWN IN CAPS (PH 10.5)
2flk THE CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP AND SOLVED FROM CRYSTALS GROWN UNDER THE SAME CONDITIONS BUT WITHOUT MG2+ AND BEF3- LIGANDS BOUND TO CHEY
2flw THE MG2+ AND BEF3--BOUND CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP BUT SOLVED FROM CRYSTALS GROWN IN HEPES (PH 7.5)
2fmf THE CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP BUT SOLVED FROM CRYSTALS GROWN IN HEPES (PH 7.5) AND WITHOUT MG2+ AND BEF3- LIGANDS BOUND TO CHEY
2fmh THE MG2+ AND BEF3--BOUND CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP BUT SOLVED FROM CRYSTALS GROWN IN TRIS (PH 8.4)
2fmi THE CHEY-CHEZ PEPTIDE COMPLEX IN THE SAME SPACE GROUP BUT SOLVED FROM CRYSTALS GROWN IN TRIS (PH 8.4) AND WITHOUT MG2+ AND BEF3- LIGANDS BOUND TO CHEY