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(-) Description

Title :  CRYSTAL STRUCTURE OF VCA0042 (L135R) 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./Biol. Unit :  A,B
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

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN VCA0042
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15C
    Expression System Strain: E. COLI BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 21-247
    Gene: VC_A0042
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
15GP8Ligand/IonGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:136 , ARG A:140 , ARG A:169 , ASN A:208 , GLN A:210 , HOH A:260 , HOH A:269 , HOH A:281 , 5GP A:502 , 5GP A:503 , 5GP A:504 , SER B:212BINDING SITE FOR RESIDUE 5GP A 501
2AC2SOFTWAREARG A:99 , GLY A:100 , GLN A:134 , ARG A:135 , ARG A:136 , HOH A:257 , HOH A:290 , HOH A:306 , 5GP A:501 , 5GP A:504BINDING SITE FOR RESIDUE 5GP A 502
3AC3SOFTWAREARG A:140 , ASP A:162 , SER A:164 , SER A:166 , GLY A:167 , CYS A:168 , ARG A:169 , CYS A:207 , ASN A:208 , GLY A:219 , LEU A:220 , GLU A:221 , HOH A:274 , HOH A:325 , HOH A:327 , HOH A:355 , 5GP A:501 , 5GP A:504BINDING SITE FOR RESIDUE 5GP A 503
4AC4SOFTWAREHOH A:10 , GLU A:101 , ARG A:135 , ARG A:136 , LYS A:137 , ARG A:140 , 5GP A:501 , 5GP A:502 , 5GP A:503BINDING SITE FOR RESIDUE 5GP A 504
5AC5SOFTWARESER A:212 , HIS A:214 , ARG B:136 , ARG B:140 , ARG B:169 , ASN B:208 , GLN B:210 , HOH B:264 , HOH B:288 , HOH B:335 , 5GP B:502 , 5GP B:503 , 5GP B:504BINDING SITE FOR RESIDUE 5GP B 501
6AC6SOFTWAREARG B:99 , GLY B:100 , GLN B:134 , ARG B:135 , ARG B:136 , HOH B:258 , HOH B:318 , HOH B:332 , HOH B:341 , HOH B:364 , HOH B:371 , 5GP B:501 , 5GP B:504BINDING SITE FOR RESIDUE 5GP B 502
7AC7SOFTWAREHIS A:214 , ARG B:140 , ASP B:162 , SER B:164 , SER B:166 , GLY B:167 , CYS B:168 , ARG B:169 , CYS B:207 , ASN B:208 , GLY B:219 , LEU B:220 , GLU B:221 , HOH B:282 , HOH B:295 , 5GP B:501 , 5GP B:504BINDING SITE FOR RESIDUE 5GP B 503
8AC8SOFTWAREHIS A:214 , GLU B:101 , ARG B:135 , ARG B:136 , LYS B:137 , ARG B:140 , HOH B:257 , HOH B:281 , 5GP B:501 , 5GP B:502 , 5GP B:503BINDING SITE FOR RESIDUE 5GP B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:117 -Pro A:118
2Glu B:117 -Pro B:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KYG)

(-) 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:227
 aligned with YCGRL_VIBCH | Q9KNC3 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
          YCGRL_VIBCH    21 SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQLRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLN 247
               SCOP domains d3kyga1 A:21-137 automated matches                                                                                   d3kyga2 A:138-247 automated matches                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhh......eeeeeee.....eeeeeeeeeeee...eeeee....hhhhhhhhh....eeeeeeee.....eeeeeeeeeeeee.....eeee....eeeeee......eeeeeeeeeee..eeeeeeeeee...eeeee............eeeeeeeee..eeee...eeeeeeeeeee...eeeeeeehhhhhhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kyg A  21 SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQRRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLN 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with YCGRL_VIBCH | Q9KNC3 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
          YCGRL_VIBCH    21 SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQLRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLN 247
               SCOP domains d3kygb1 B:21-137 automated matches                                                                                   d3kygb2 B:138-247 automated matches                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------YcgR_2-3kygB03 B:36-127                                                                     ------PilZ-3kygB01 B:134-239                                                                                    -------- Pfam domains (1)
           Pfam domains (2) ---------------YcgR_2-3kygB04 B:36-127                                                                     ------PilZ-3kygB02 B:134-239                                                                                    -------- Pfam domains (2)
         Sec.struct. author ..eeeeeehhhhhhh.....eeeeeee.....eeeeeeeeeeee...eeeee....hhhhhhhhh....eeeeeeee.....eeeeeeeeeeeee.....eeee....eeeeee......eeeeeeeeeee..eeeeeeeeee...eeeee............eeeeeeeee..eeee...eeeeeeeeeee...eeeeeeehhhhhhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kyg B  21 SKTVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQRRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLN 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KYG)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PilZ] (4)
(-)
Family: PilZ (4)
(-)
Vibrio cholerae (2)
1aPilZ-3kygB01B:134-239
1bPilZ-3kygB02B:134-239
(-)
Clan: no clan defined [family: YcgR_2] (2)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YCGRL_VIBCH | Q9KNC3)
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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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.
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.
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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        YCGRL_VIBCH | Q9KNC3: 1yln

(-) Related Entries Specified in the PDB File

3kyg