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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE MOLECULAR MECHANISM OF H-NOX ACTIVATION
 
Authors :  C. Olea Jr, M. A. Herzik Jr, J. Kuriyan, M. A. Marletta
Date :  06 Jan 10  (Deposition) - 16 Mar 10  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Olea, M. A. Herzik, J. Kuriyan, M. A. Marletta
Structural Insights Into The Molecular Mechanism Of H-Nox Activation.
Protein Sci. V. 19 881 2010
PubMed-ID: 20162612  |  Reference-DOI: 10.1002/PRO.357

(-) Compounds

Molecule 1 - METHYL-ACCEPTING CHEMOTAXIS PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-188
    Gene: TAR4, TTE0680
    Mutation: YES
    Organism Scientific: THERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid: 119072

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD6Ligand/IonIMIDAZOLE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , LYS A:2 , ILE A:5 , PHE A:78 , TYR A:85 , PHE A:86 , PHE A:94 , MET A:98 , LEU A:105 , ALA A:112 , THR A:113 , PRO A:114 , PRO A:115 , LEU A:117 , TYR A:131 , SER A:133 , ARG A:135 , MET A:137 , LEU A:144 , HOH A:206 , IMD A:501 , IMD A:502BINDING SITE FOR RESIDUE HEM A 200
2AC2SOFTWAREILE A:5 , TYR A:140 , LEU A:144 , HEM A:200BINDING SITE FOR RESIDUE IMD A 501
3AC3SOFTWAREMET A:98 , GLY A:102 , PRO A:115 , LEU A:117 , HEM A:200BINDING SITE FOR RESIDUE IMD A 502
4AC4SOFTWAREILE B:5 , TYR B:140 , HEM B:200BINDING SITE FOR RESIDUE IMD B 501
5AC5SOFTWAREMET B:98 , GLY B:102 , PRO B:114 , PRO B:115 , LEU B:117 , HEM B:200BINDING SITE FOR RESIDUE IMD B 502
6AC6SOFTWAREMET B:1 , LYS B:2 , TYR B:85 , PHE B:86 , PHE B:94 , LEU B:105 , ALA B:112 , THR B:113 , PRO B:114 , PRO B:115 , TYR B:131 , SER B:133 , MET B:137 , TYR B:140 , HOH B:205 , IMD B:501 , IMD B:502BINDING SITE FOR RESIDUE HEM B 200
7AC7SOFTWAREILE C:5 , ASN C:74 , PHE C:78 , TYR C:140 , HEM C:200 , IMD C:502BINDING SITE FOR RESIDUE IMD C 501
8AC8SOFTWAREMET C:98 , PRO C:114 , PRO C:115 , LEU C:117 , HEM C:200 , IMD C:501BINDING SITE FOR RESIDUE IMD C 502
9AC9SOFTWARELYS C:2 , ILE C:5 , PHE C:78 , TYR C:85 , MET C:98 , LEU C:105 , ALA C:112 , THR C:113 , PRO C:114 , PRO C:115 , TYR C:131 , SER C:133 , ARG C:135 , MET C:137 , HOH C:198 , HOH C:212 , IMD C:501 , IMD C:502BINDING SITE FOR RESIDUE HEM C 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LAI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LAI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LAI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LAI)

(-) Exons   (0, 0)

(no "Exon" information available for 3LAI)

(-) 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:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3laia_ A: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3laiA00 A:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lai A   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVGLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d3laib_ B: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains 3laiB00 B:1-188 H-NOX domain                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lai B   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVGLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEY 185
               SCOP domains d3laic_ C: Methyl-accepting chemotaxis protein                                                                                                                                            SCOP domains
               CATH domains 3laiC00 C:1-185 H-NOX domain                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........eeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lai C   1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVGLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEY 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LAI)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8RBX6_CALS4 | Q8RBX6)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Q8RBX6_CALS4 | Q8RBX6
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 Related Entries

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

UniProtKB/TrEMBL
        Q8RBX6_CALS4 | Q8RBX6: 1u4h 1u55 1u56 1xbn 3eee 3iqb 3lah 3m0b 3nvr 3nvu 3sj5 3tf0 3tf1 4fdk 4it2 5jru 5jrv 5jrx

(-) Related Entries Specified in the PDB File

1u4h 1u55 1u56 3eee 3iqb 3lah