1YLN - JenaLib

Title :   THE CRYSTAL STRUCTURE OF THE PROTEIN OF UNKNOWN FUNCTION VCA0042 FROM VIBRIO CHOLERAE O1

Authors :   R. Zhang, M. Zhou, S. Moy, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

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

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Vibrio Cholerae O1, Beta Barrels, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, M. Zhou, S. Moy, F. Collart, A. Joachimiak
The Crystal Structure Of The Hypothetical Protein Vca0042 From Vibrio Cholerae O1
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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:226
 aligned with YCGRL_VIBCH | Q9KNC3 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:226
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
          YCGRL_VIBCH    23 TVSTINSTDALAMVEHSSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQLRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLNA 248
               SCOP domains d1ylna2 A:23-137 Hypothetical protein VCA0042, N-terminal domain                                                   d1ylna1 A:138-248 Hypothetical protein VCA0042, C-terminal domain                                               SCOP domains
               CATH domains 1ylnA01 A:23-136 Electron Transport, Fmn-binding Protein; Chain A                                                 1ylnA02 A:137-248 predicted glycosyltransferase like domains                                                     CATH domains
               Pfam domains -------------YcgR_2-1ylnA02 A:36-127                                                                     ------PilZ-1ylnA01 A:134-239                                                                                    --------- Pfam domains
         Sec.struct. author ..eeeehhhhhhh.....eeeeeee.....eeeeeeeeeeee...eeeee....hhhhhhhhh....eeeeeeee.....eeeeeeeeeeeee.....eeee....eeeeee......eeeeeeeeeee..eeeeeeeeee...eeeeee...........eeeeee............eeeeeeeeee....eeeeeeehhhhhhhhhhhhhheee....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yln A  23 TVSTINSTDALAMVEHsSELTLSITTPVGTKFVCRTPFIGTHTDKFLLVEMPKISADDLQYFFQEGFWMNIRAISPRGEGALIHFRSQLMHILQEPVPMAFLSIPNTMQVSQLRKEPRFELNLAGKVLFDEHRGDCELRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGTKTFPPLTGKICNLQRSLHHARYGLEFNEEGRNNAKNLLAQLKFNGTKLTLNA 248
                                    32      | 42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
                                           39-OSE

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	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, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (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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