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Asym./Biol. Unit (Jmol Viewer)

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Title :   M. LOTI CYCLIC-NUCLEOTIDE BINDING DOMAIN MUTANT 2

Authors :   G. M. Clayton, S. L. Altieri, L. R. Thomas, J. H. Morais-Cabral

Date :   19 Mar 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,C

Keywords :   Mlotik1 Cyclic-Nucleotide Binding Domain Mutant 2. Cyclic- Amp Bound, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Altieri, G. M. Clayton, W. R. Silverman, A. O. Olivares, E. M. De La Cruz, L. R. Thomas, J. H. Morais-Cabral
Structural And Energetic Analysis Of Activation By A Cyclic Nucleotide Binding Domain.
J. Mol. Biol. V. 381 655 2008
PubMed-ID: 18619611 | Reference-DOI: 10.1016/J.JMB.2008.06.011
(for further references see the PDB file header)

Molecule 1 - MLL3241 PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T
	Expression System Vector Type	:	PLASMID
	Fragment	:	CYCLIC-NUCLEOTIDE BINDING DOMAIN, UNP RESIDUES 216-355
	Mutation	:	YES
	Organism Scientific	:	RHIZOBIUM LOTI

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CMP	2	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:282 , THR A:284 , PHE A:296 , GLY A:297 , GLU A:298 , MET A:299 , ALA A:300 , GLU A:307 , SER A:308 , ALA A:309 , VAL A:311 , ARG A:348 , HOH A:364 , HOH A:370 , HOH A:374 , HOH A:394	BINDING SITE FOR RESIDUE CMP A 1
2	AC2	SOFTWARE	HOH C:101 , HOH C:107 , HOH C:132 , VAL C:282 , VAL C:288 , PHE C:296 , GLY C:297 , GLU C:298 , MET C:299 , ALA C:300 , GLU C:307 , SER C:308 , ALA C:309 , VAL C:311 , ARG C:348	BINDING SITE FOR RESIDUE CMP C 2

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

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

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CNGK1_RHILO	235-348	2	A:235-348 C:235-348
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CNGK1_RHILO	262-278	2	A:262-278 C:262-278
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CNGK1_RHILO	296-313	2	A:296-313 C:296-313

(no "Exon" information available for 3CLP)

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:132
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:132
                                   227       237       247       257       267       277       287       297       307       317       327       337       347  
          CNGK1_RHILO   218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
               SCOP domains d3clpa_ A: automated matches                                                                                                         SCOP domains
               CATH domains 3clpA00 A:218-349 Jelly Rolls                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------CNMP_BINDING_3  PDB: A:235-348 UniProt: 235-348                                                                   - PROSITE (1)
                PROSITE (2) --------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3clp A 218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPESATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
                                   227       237       247       257       267       277       287       297       307       317       327       337       347

Chain C from PDB  Type:PROTEIN  Length:133
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:133
                                   227       237       247       257       267       277       287       297       307       317       327       337       347   
          CNGK1_RHILO   218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
               SCOP domains d3clpc_ C: automated matches                                                                                                          SCOP domains
               CATH domains 3clpC00 C:218-350 Jelly Rolls                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------CNMP_BINDING_3  PDB: C:235-348 UniProt: 235-348                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3clp C 218 VRRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPESATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERRG 350
                                   227       237       247       257       267       277       287       297       307       317       327       337       347

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: cAMP-binding domain (78)

Protein domain: automated matches (22)

Rhizobium loti [TaxId: 381] (3)

1a	d3clpa_	A:
1b	d3clpc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Rhizobium loti. (2)

1a	3clpC00	C:218-350
1b	3clpA00	A:218-349

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (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.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	CNGK1_RHILO \| Q98GN8	:	1u12 1vp6 2k0g 2kxl 2zd9 3beh 3cl1 3co2 4chv 4chw 4muv

1u12	M.LOTI ION CHANNEL CYCLIC NUCLEOTIDE BINDING DOMAIN MUTANT
1vp6	M.LOTI ION CHANNEL CYLIC NUCLEOTIDE BINDING DOMAIN
3beh	STRUCTURE OF A BACTERIAL CYCLIC NUCLEOTIDE REGULATED ION CHANNEL
3cl1	M.LOTI ION CHANNEL CYLIC NUCLEOTIDE BINDING DOMAIN, CYCLIC- GMP BOUND
3co2	MLOTIK1 ION CHANNEL CYCLIC-NUCLEOTIDE BINDING DOMAIN MUTANT

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

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