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(-) Description

Title :  CO-BOUND STRUCTURE OF BJFIXLH
 
Authors :  R. A. Ayers, K. Moffat
Date :  04 Jun 08  (Deposition) - 04 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Signaling Protein, Transferase, Phosphoprotein, Nitrogen Fixation, Per-Arnt-Sim, Pas, Kinase, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Ayers, K. Moffat
Changes In Quaternary Structure In The Signaling Mechanisms Of Pas Domains.
Biochemistry V. 47 12078 2008
PubMed-ID: 18942854  |  Reference-DOI: 10.1021/BI801254C

(-) Compounds

Molecule 1 - SENSOR PROTEIN FIXL
    Chains: A, B, C, D
    EC Number: 2.7.13.3, 2.7.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HEME DOMAIN, RESIDUES 151-269
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 375
    Synonym: BJFIXLH FIXL

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CMO4Ligand/IonCARBON MONOXIDE
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NA1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:157 , ILE A:159 , VAL A:188 , LEU A:191 , MET A:192 , ASP A:196 , HIS A:200 , TYR A:203 , ARG A:206 , TYR A:207 , HIS A:214 , ILE A:215 , ILE A:216 , ARG A:220 , VAL A:222 , THR A:223 , LEU A:236 , ILE A:238 , PHE A:249 , GLY A:251 , CMO A:1259 , HOH A:2066BINDING SITE FOR RESIDUE HEM A1258
02AC2SOFTWAREILE B:157 , ILE B:159 , LEU B:191 , MET B:192 , ASP B:196 , HIS B:200 , TYR B:203 , ARG B:206 , TYR B:207 , PRO B:213 , HIS B:214 , ILE B:215 , ILE B:216 , ARG B:220 , VAL B:222 , THR B:223 , MET B:234 , LEU B:236 , ILE B:238 , PHE B:249 , CMO B:1260 , HOH B:2120BINDING SITE FOR RESIDUE HEM B1259
03AC3SOFTWAREILE C:157 , ILE C:159 , VAL C:188 , LEU C:191 , MET C:192 , ASP C:196 , HIS C:200 , TYR C:203 , ILE C:204 , TYR C:207 , HIS C:214 , ILE C:215 , ILE C:216 , ARG C:220 , VAL C:222 , THR C:223 , MET C:234 , LEU C:236 , ILE C:238 , PHE C:249 , GLY C:251 , CMO C:1260 , HOH C:2123 , HOH C:2124 , HOH C:2125BINDING SITE FOR RESIDUE HEM C1259
04AC4SOFTWAREHOH B:2022 , ILE D:157 , ILE D:159 , VAL D:188 , LEU D:191 , MET D:192 , ASP D:196 , HIS D:200 , TYR D:203 , TYR D:207 , PRO D:213 , HIS D:214 , ILE D:215 , ILE D:216 , ARG D:220 , VAL D:222 , THR D:223 , MET D:234 , LEU D:236 , ILE D:238 , PHE D:249 , GLY D:251 , CMO D:1260BINDING SITE FOR RESIDUE HEM D1259
05AC5SOFTWAREILE A:215 , LEU A:236 , ILE A:238 , HEM A:1258BINDING SITE FOR RESIDUE CMO A1259
06AC6SOFTWAREILE B:215 , LEU B:236 , ILE B:238 , HEM B:1259BINDING SITE FOR RESIDUE CMO B1260
07AC7SOFTWAREILE C:215 , LEU C:236 , ILE C:238 , HEM C:1259BINDING SITE FOR RESIDUE CMO C1260
08AC8SOFTWAREILE D:215 , LEU D:236 , ILE D:238 , HEM D:1259BINDING SITE FOR RESIDUE CMO D1260
09AC9SOFTWARELEU A:181 , GLU A:182 , ILE A:184 , HOH A:2037 , LEU C:181 , GLU C:182 , ILE C:184 , HOH C:2029BINDING SITE FOR RESIDUE NA C1261
10BC1SOFTWARESER C:237 , HOH C:2077 , SER D:243 , GLY D:244BINDING SITE FOR RESIDUE CL C1262
11BC2SOFTWAREARG A:220 , ILE A:221 , ARG C:254 , HOH C:2077 , HOH C:2105 , GLY D:244BINDING SITE FOR RESIDUE CL C1263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VV8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:194 -Pro A:195
2Glu B:194 -Pro B:195
3Glu C:194 -Pro C:195
4Glu D:194 -Pro D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VV8)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PACPS50113 PAC domain profile.FIXL_BRADU88-140
209-268
 
 
 		  4-
A:209-257
B:209-258
C:209-258
D:209-258

(-) Exons   (0, 0)

(no "Exon" information available for 2VV8)

(-) 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:106
 aligned with FIXL_BRADU | P23222 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:106
                                   161       171       181       191       201       211       221       231       241       251      
           FIXL_BRADU   152 IPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLT 257
               SCOP domains d2vv8a_ A: Histidine kinase FixL heme domain                                                               SCOP domains
               CATH domains 2vv8A00 A:152-257  [code=3.30.450.20, no name defined]                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh..hhhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------PAC  PDB: A:209-257 UniProt: 209-268              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2vv8 A 152 IPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLT 257
                                   161       171       181       191       201       211       221       231       241       251      


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with FIXL_BRADU | P23222 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:107
                                   161       171       181       191       201       211       221       231       241       251       
           FIXL_BRADU   152 IPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
               SCOP domains d2vv8b_ B: Histidine kinase FixL heme domain                                                                SCOP domains
               CATH domains 2vv8B00 B:152-258  [code=3.30.450.20, no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh..hhhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------PAC  PDB: B:209-258 UniProt: 209-268               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2vv8 B 152 IPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
                                   161       171       181       191       201       211       221       231       241       251       


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with FIXL_BRADU | P23222 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:106
                                   162       172       182       192       202       212       222       232       242       252      
           FIXL_BRADU   153 PDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
               SCOP domains d2vv8c_ C: Histidine kinase FixL heme domain                                                               SCOP domains
               CATH domains 2vv8C00 C:153-258  [code=3.30.450.20, no name defined]                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh..hhhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------PAC  PDB: C:209-258 UniProt: 209-268               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2vv8 C 153 PDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
                                   162       172       182       192       202       212       222       232       242       252      


Chain D from PDB  Type:PROTEIN  Length:108
 aligned with FIXL_BRADU | P23222 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:108
                                   160       170       180       190       200       210       220       230       240       250        
           FIXL_BRADU   151 TIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
               SCOP domains d2vv8d_ D: Histidine kinase FixL heme domain                                                                 SCOP domains
               CATH domains 2vv8D00 D:151-258  [code=3.30.450.20, no name defined]                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhh..hhhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PAC  PDB: D:209-258 UniProt: 209-268               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2vv8 D 151 TIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTE 258
                                   160       170       180       190       200       210       220       230       240       250
   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  (0, 0)

(no "Pfam Domain" information available for 2VV8)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (FIXL_BRADU | P23222)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    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:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
    GO:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    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.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  2vv8
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  FIXL_BRADU | P23222
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 Related Entries

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

UniProtKB/Swiss-Prot
        FIXL_BRADU | P23222: 1dp6 1dp8 1dp9 1drm 1lsv 1lsw 1lsx 1lt0 1xj2 1xj3 1xj4 1xj6 1y28 2cmn 2owh 2owj 2vv6 2vv7 4gcz

(-) Related Entries Specified in the PDB File

1dp6 OXYGEN-BINDING COMPLEX OF FIXL HEME DOMAIN
1dp8 CRYSTAL STRUCTURE OF THE NITRIC OXIDE BOUND FIXL HEME DOMAIN
1dp9 CRYSTAL STRUCTURE OF IMIDAZOLE-BOUND FIXL HEME DOMAIN
1drm CRYSTAL STRUCTURE OF THE LIGAND FREE BJFIXL HEME DOMAIN
1lsv CRYSTAL STRUCTURE OF THE CO-BOUND BJFIXL HEME DOMAIN
1lsw CRYSTAL STRUCTURE OF THE FERROUS BJFIXL HEME DOMAIN
1lsx CRYSTAL STRUCTURE OF THE METHYLIMIDAZOLE-BOUND BJFIXL HEMEDOMAIN
1lt0 CRYSTAL STRUCTURE OF THE CN-BOUND BJFIXL HEME DOMAIN
1xj2 CO-BOUND STRUCTURE OF BJFIXLH
1xj3 BJFIXLH IN UNLIGANDED FERROUS FORM
1xj4 CO-BOUND STRUCTURE OF BJFIXLH
1xj6 STRUCTURE OF BJFIXLH IN THE UNLIGANDED FERROUS FORM
1y28 CRYSTAL STRUCTURE OF THE R220A METBJFIXL HEME DOMAIN
2cmn A PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR
2vv6 MOLECULAR MECHANISM OF SIGNAL TRANSDUCTION IN BJFIXL
2vv7 MOLECULAR MECHANISM OF SIGNAL TRANSDUCTION IN BJFIXL