2YX0 - JenaLib

Title :   CRYSTAL STRUCTURE OF P. HORIKOSHII TYW1

Authors :   S. Goto-Ito, R. Ishii, T. Ito, R. Shibata, E. Fusatomi, S. Sekine, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   23 Apr 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

Chains :   Asym./Biol. Unit : A

Keywords :   Radical Sam Enzyme, Predicted Trna Modification Enzyme, Metal Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Goto-Ito, R. Ishii, T. Ito, R. Shibata, E. Fusatomi, S. Sekine, Y. Bessho, S. Yokoyama
Structure Of An Archaeal Tyw1, The Enzyme Catalyzing The Second Step Of Wye-Base Biosynthesis
Acta Crystallogr. , Sect. D V. 63 1059 2007
PubMed-ID: 17881823 | Reference-DOI: 10.1107/S0907444907040668
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:324
 aligned with TYW1_PYRHO | O59412 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:332
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
           TYW1_PYRHO    11 KITVQANPNMPKEVAELFRKQHYEIVGRHSGVKLCHWLKKSLTEGRFCYKQKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEAWNPTHAAISLSGEPMLYPYMGDLVEEFHKRGFTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERILRFLELMRDLPTRTVVRLTLVKGENMHSPEKYAKLILKARPMFVEAKAYMFVGYSRNRLTINNMPSHQDIREFAEALVKHLPGYHIEDEYEPSRVVLIMRDDVDPQGTGVEGRFIKH 342
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------Fer4_12-2yx0A01 A:69-216                                                                                                                            ----------------------------------------------Wyosine_form-      2yx0A03 A:263-325                           ----------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------Radical_SAM-2yx0A02 A:75-261                                                                                                                                                               --------------      ------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhhh..eee...eee....hhhhhhhhh..hhhhhhhh.hhh.eeeee..............................hhhhhhhhhhhhhhhhhh...--...hhhhhhhhh...eeee....hhhhh.hhhhhhhhhhhh..eeeeee...hhhhhhhhhhh.....eeeeee...hhhhhhhhhh....hhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhh..eeeeee..------...hhhhh.hhhhhhhhhhhhhh....eeeeeeehhh.eeeeee...eeeee...eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yx0 A  11 KITVQANPNMPKEVAELFRKQHYEIVGRHSGVKLCHWLKKSLTEGRFCYKQKFYGIHSHRCLQMTPVLAWCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYK--PKVDKKKFEEAWNPTHAAISLSGEPMLYPYMGDLVEEFHKRGFTTFIVTNGTIPERLEEMIKEDKLPTQLYVSITAPDIETYNSVNIPMIPDGWERILRFLELMRDLPTRTVVRLTLVKGENMHSPEKYAKLILKARPMFVEAKAYM------NRLTINNMPSHQDIREFAEALVKHLPGYHIEDEYEPSRVVLIMRDDVDPQGTGVEGRFIKH 342
                                    20        30        40        50        60        70        80        90       100       110       120     | 130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    |    - |     290       300       310       320       330       340  
                                                                                                                                             126  |                                                                                                                                               275    282                                                            
                                                                                                                                                129

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 (3, 3)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TYW1_PYRHO | O59412)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016833	oxo-acid-lyase activity	Catalysis of the cleavage of a C-C bond by other means than by hydrolysis or oxidation, of a 3-hydroxy acid.
biological process
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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