3KYF - JenaLib

Title :   CRYSTAL STRUCTURE OF P4397 COMPLEXED WITH C-DI-GMP

Authors :   K. S. Ryu, J. Ko, H. Kim, B. S. Choi

Date :   06 Dec 09 (Deposition) - 14 Apr 10 (Release) - 14 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   C-Di-Gmp, Pilz Domain, Pp4397, Vca0042, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ko, K. S. Ryu, H. Kim, J. S. Shin, J. O. Lee, C. Cheong, B. S. Choi
Structure Of Pp4397 Reveals The Molecular Basis For Different C-Di-Gmp Binding Modes By Pilz Domain Proteins.
J. Mol. Biol. V. 398 97 2010
PubMed-ID: 20226196 | Reference-DOI: 10.1016/J.JMB.2010.03.007

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:123 , ARG A:127 , HIS A:201 , HOH A:271 , HOH A:274 , HOH A:288 , HOH A:325 , 5GP A:502 , 5GP A:503 , 5GP A:504	BINDING SITE FOR RESIDUE 5GP A 501
2	AC2	SOFTWARE	PHE A:84 , GLY A:87 , GLN A:121 , ARG A:122 , ARG A:123 , HOH A:300 , HOH A:319 , HOH A:322 , 5GP A:501 , 5GP A:504	BINDING SITE FOR RESIDUE 5GP A 502
3	AC3	SOFTWARE	ARG A:127 , ASP A:157 , SER A:159 , THR A:161 , GLY A:162 , CYS A:163 , LYS A:164 , ARG A:200 , HIS A:201 , GLY A:214 , VAL A:215 , ARG A:216 , HOH A:271 , HOH A:394 , 5GP A:501 , 5GP A:504	BINDING SITE FOR RESIDUE 5GP A 503
4	AC4	SOFTWARE	ARG A:122 , ARG A:123 , ASN A:124 , ARG A:127 , HOH A:250 , HOH A:272 , HOH A:379 , 5GP A:501 , 5GP A:502 , 5GP A:503	BINDING SITE FOR RESIDUE 5GP A 504

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:231
 aligned with YCGR_PSEPK | Q88EQ6 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:231
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237 
           YCGR_PSEPK     8 PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDGVRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRFEGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQRE 238
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----YcgR-3kyfA02 A:12-120                                                                                        PilZ-3kyfA01 A:121-234                                                                                            ---- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhh...eeeee.....eeee.eeeee....eeeee...hhhhhhhhhh...eeeeeee..eeeeeee....eeeee..eeeeee.....eeee.......ee.hhhhh.eeee..........eeeeeeee...eeeeeee..hhhhh....eeeeeee.....eeeeeeeeeeeeeehhh.eeeeeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kyf A   8 PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDGVRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRFEGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQRE 238
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (YCGR_PSEPK | Q88EQ6)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0035438	cyclic-di-GMP binding	Interacting selectively and non-covalently with cyclic-di-GMP, cyclic dimeric guanosine monophosphate.
	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:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0071973	bacterial-type flagellum-dependent cell motility	Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0071945	regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed	A process that modulates flagellum-dependent motility in bacteria by modulating the speed or direction of rotation of a rotary flagellar motor, mediated by interactions between the braking protein.
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:0009425	bacterial-type flagellum basal body	One of the three major substructures of the flagellin-based flagellum; a structure consisting of a rod, a series of rings, the Mot proteins, the switch complex and the flagellum-specific export apparatus. The rings anchor the flagellum to the cytoplasmic membrane (MS ring), the peptidoglycan (P ring) and the outer membrane (L ring). Examples of this component are found in bacteria.

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