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(-) Description

Title :  M. LOTI CYCLIC NUCLEOTIDE BINDING DOMAIN MUTANT
 
Authors :  G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral
Date :  14 Jul 04  (Deposition) - 30 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mutant Cyclic Nucleotide Binding Domain, C-Helix Mutation, Unliganded, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral
Structural Basis Of Ligand Activation In A Cyclic Nucleotid Regulated Potassium Channel
Cell(Cambridge, Mass. ) V. 119 615 2004
PubMed-ID: 15550244  |  Reference-DOI: 10.1016/J.CELL.2004.10.030

(-) Compounds

Molecule 1 - CYCLIC NUCLEOTIDE BINDING DOMAIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T
    Expression System Strain: BL21-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CYCLIC NUCLEOTIDE BINDING DOMAIN, CYTOPLASMIC DOMAIN
    Mutation: YES
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 37)

Asymmetric/Biological Unit (3, 37)
No.NameCountTypeFull Name
1IOD31Ligand/IonIODIDE ION
2K4Ligand/IonPOTASSIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:242BINDING SITE FOR RESIDUE IOD B 211
02AC2SOFTWARELYS A:238BINDING SITE FOR RESIDUE IOD A 356
03AC3SOFTWAREARG A:271 , ARG B:307BINDING SITE FOR RESIDUE IOD A 411
04AC4SOFTWARESER A:281 , PRO A:287BINDING SITE FOR RESIDUE IOD A 511
05AC5SOFTWAREARG A:307 , ARG B:271BINDING SITE FOR RESIDUE IOD A 611
06AC6SOFTWAREPHE A:223 , ARG A:249BINDING SITE FOR RESIDUE IOD A 711
07AC7SOFTWARELEU A:229BINDING SITE FOR RESIDUE IOD A 811
08AC8SOFTWAREPRO B:234BINDING SITE FOR RESIDUE IOD B 911
09AC9SOFTWAREGLY B:221BINDING SITE FOR RESIDUE IOD B 112
10BC1SOFTWAREPRO A:257 , THR B:255BINDING SITE FOR RESIDUE IOD B 122
11BC2SOFTWAREALA A:325 , GLN A:328BINDING SITE FOR RESIDUE IOD A 132
12BC3SOFTWAREPRO A:234BINDING SITE FOR RESIDUE IOD A 142
13BC4SOFTWARESER A:303BINDING SITE FOR RESIDUE IOD A 192
14BC5SOFTWARETHR A:255 , THR B:255BINDING SITE FOR RESIDUE IOD B 212
15BC6SOFTWAREGLU A:347BINDING SITE FOR RESIDUE IOD A 812
16BC7SOFTWAREPRO B:306BINDING SITE FOR RESIDUE IOD B 913
17BC8SOFTWAREPHE B:223 , IOD B:918BINDING SITE FOR RESIDUE IOD B 914
18BC9SOFTWAREHOH B:8BINDING SITE FOR RESIDUE IOD B 915
19CC1SOFTWARESO4 A:145 , ARG A:254 , PHE B:273BINDING SITE FOR RESIDUE IOD B 916
20CC2SOFTWAREARG B:249 , IOD B:914BINDING SITE FOR RESIDUE IOD B 918
21CC3SOFTWAREGLN B:328BINDING SITE FOR RESIDUE IOD B 919
22CC4SOFTWARECYS A:263 , GLY A:297 , ARG A:307 , SER A:308 , ALA A:309 , K A:455BINDING SITE FOR RESIDUE SO4 A 144
23CC5SOFTWAREARG A:254 , ARG A:271 , PHE A:273 , SER A:321 , ARG B:254 , ARG B:271 , IOD B:916BINDING SITE FOR RESIDUE SO4 A 145
24CC6SOFTWAREGLY A:291BINDING SITE FOR RESIDUE K A 155
25CC7SOFTWAREPRO B:287BINDING SITE FOR RESIDUE K B 920
26CC8SOFTWARESER A:279BINDING SITE FOR RESIDUE K A 814
27CC9SOFTWARESO4 A:144BINDING SITE FOR RESIDUE K A 455

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U12)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CNGK1_RHILO235-348
 		  2A:235-347
B:235-347
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CNGK1_RHILO262-278
 		  2A:262-278
B:262-278
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CNGK1_RHILO296-313
 		  2A:296-313
B:296-313

(-) Exons   (0, 0)

(no "Exon" information available for 1U12)

(-) 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:131
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:131
                                   228       238       248       258       268       278       288       298       308       318       328       338       348 
          CNGK1_RHILO   219 RRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
               SCOP domains d1u12a_ A: Putative ion channel CnbD                                                                                                SCOP domains
               CATH domains 1u12A00 A:219-349 Jelly Rolls                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhhhhhhh..eeeee....eee.......eeeeeee..eeee....eee....eehhhhhh.......eeee...eeeeeeehhhhhhhhh...........hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------CNMP_BINDING_3  PDB: A:235-347 UniProt: 235-348                                                                   - PROSITE (1)
                PROSITE (2) -------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u12 A 219 RRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALEAR 349
                                   228       238       248       258       268       278       288       298       308       318       328       338       348 


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:127
                                   230       240       250       260       270       280       290       300       310       320       330       340       
          CNGK1_RHILO   221 GDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALE 347
               SCOP domains d1u12b_ B: Putative ion channel CnbD                                                                                            SCOP domains
               CATH domains 1u12B00 B:221-347 Jelly Rolls                                                                                                   CATH domains
           Pfam domains (1) --------------------------------cNMP_binding-1u12B01 B:253-336                                                      ----------- Pfam domains (1)
           Pfam domains (2) --------------------------------cNMP_binding-1u12B02 B:253-336                                                      ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeee....eee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------CNMP_BINDING_3  PDB: B:235-347 UniProt: 235-348                                                                   PROSITE (1)
                PROSITE (2) -----------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ---------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u12 B 221 GDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALE 347
                                   230       240       250       260       270       280       290       300       310       320       330       340
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CNGK1_RHILO | Q98GN8)
molecular function
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    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:0005267    potassium channel activity    Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005249    voltage-gated potassium channel activity    Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0008076    voltage-gated potassium channel complex    A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CNGK1_RHILO | Q98GN8: 1vp6 2k0g 2kxl 2zd9 3beh 3cl1 3clp 3co2 4chv 4chw 4muv

(-) Related Entries Specified in the PDB File

1pf0 M. LOTI CYCLIC NUCLEOTIDE BINDING DOMAIN