2PGE - JenaLib

Title :   CRYSTAL STRUCTURE OF MENC FROM DESULFOTALEA PSYCHROPHILA LSV54

Authors :   R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   09 Apr 07 (Deposition) - 24 Apr 07 (Release) - 13 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Menc, Osbs, 9393A, Nysgxrc, Psi-Ii, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Odokonyero, A. Sakai, Y. Patskovsky, V. N. Malashkevich, A. A. Fedorov, J. B. Bonanno, E. V. Fedorov, R. Toro, R. Agarwal, C. Wang N. D. Ozerova, W. S. Yew, J. M. Sauder, S. Swaminathan, S. K. Burley, S. C. Almo, M. E. Glasner
Loss Of Quaternary Structure Is Associated With Rapid Sequence Divergence In The Osbs Family.
Proc. Natl. Acad. Sci. Usa V. 111 8535 2014
PubMed-ID: 24872444 | Reference-DOI: 10.1073/PNAS.1318703111

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:356
 aligned with Q6ARP5_DESPS | Q6ARP5 from UniProtKB/TrEMBL  Length:368

    Alignment length:366
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
         Q6ARP5_DESPS     2 SGMELSYRRSDLIFKRPAGTSRGVLTSKPTWFVRLDIDGHGGQGEVSLIPGLSLDPEEQIGRELDLLARRLRAEEPIRLRQFLAERGGADFSDYRSVLTDIAGILDSWQVSTDGRFPALRFALEMALLDLLSGGRQEWFASDFTRGEKRIPVNGLIWMGEAAFMQEQIEAKLAEGYGCLKLKIGAIDFDKECALLAGIRESFSPQQLEIRVDANGAFSPANAPQRLKRLSQFHLHSIEQPIRQHQWSEMAALCANSPLAIALDEELIGLGAEQRSAMLDAIRPQYIILKPSLLGGFHYAGQWIELARERGIGFWITSALESNLGLAAIAQWTALYQPTMPQGLGTGQLYTNNLPSNLAVDGGLLGV 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2pgeA01 A:3-136        Enolase-like, N-terminal domain                                                                                2pgeA02 A:137-368 Enolase superfamily                                                                                                                                                                                                    CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE-2pgeA01 A:196-265                                              ------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-2pgeA02 A:265-367                                                                             - Pfam domains (2)
         Sec.struct. author ...eeeeee..ee...-------...ee.eeeeeeee..eeeeeeee........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh................ee..eee...hhhhhhhhhhhhhhh...eeeee.---hhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhh....eee......hhhhhhhhhhhh...eeehhhhh...hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.......................ee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pge A   3 SGMELSYRRSDLIFKR-------VLTSKPTWFVRLDIDGHGGQGEVSLIPGLSLDPEEQIGRELDLLARRLRAEEPIRLRQFLAERGGADFSDYRSVLTDIAGILDSWQVSTDGRFPALRFALEMALLDLLSGGRQEWFASDFTRGEKRIPVNGLIWMGEAAFMQEQIEAKLAEGYGCLKLKI---DFDKECALLAGIRESFSPQQLEIRVDANGAFSPANAPQRLKRLSQFHLHSIEQPIRQHQWSEMAALCANSPLAIALDEELIGLGAEQRSAMLDAIRPQYIILKPSLLGGFHYAGQWIELARERGIGFWITSALESNLGLAAIAQWTALYQPTMPQGLGTGQLYTNNLPSNLAVDGGLLGV 368
                                    12     |   -   |    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  |   |192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
                                          18      26                                                                                                                                                            185 189

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 (2, 2)

Pfam Domains (2, 2)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q6ARP5_DESPS | Q6ARP5)

molecular function
	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: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.
biological process
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
	GO:0009234	menaquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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	2pge
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