3UWQ - JenaLib

Title :   1.80 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH URIDINE-5'-MONOPHOSPHATE (UMP)

Authors :   A. S. Halavaty, G. Minasov, J. Winsor, L. Shuvalova, M. Kuhn, E. V. Filip L. Papazisi, W. F. Anderson, Center For Structural Genomics Of I Diseases (Csgid)

Date :   02 Dec 11 (Deposition) - 14 Dec 11 (Release) - 14 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Orotidine 5'-Phosphate Decarboxylase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Decarboxylase, Lyase, Pyrimidine Biosynthesis, Csgid, Uridine-5'-Monophosphate, Tim-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Halavaty, G. Minasov, J. Winsor, L. Shuvalova, M. Kuhn, E. V. Filippova, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 80 Angstrom Resolution Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Uridine-5'-Monophosphate (Ump)
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:9 , ASP A:11 , LYS A:33 , THR A:120 , PRO A:178 , GLY A:179 , ARG A:181 , VAL A:208 , ILE A:209 , GLY A:210 , ARG A:211 , PGE A:236 , HOH A:267 , HOH A:277 , HOH A:288 , HOH A:296 , HOH A:302 , HOH A:331 , ILE B:66 , HOH B:249	BINDING SITE FOR RESIDUE U5P A 232
02	AC2	SOFTWARE	ILE A:66 , ASN A:68 , SER A:71 , LYS A:72 , HOH A:346 , HOH A:397 , HOH A:439 , HOH A:478 , HOH A:483 , TYR B:12 , ARG B:211 , THR B:214 , HOH B:304 , HOH B:465	BINDING SITE FOR RESIDUE XPE A 233
03	AC3	SOFTWARE	ASP A:11 , GLN A:215	BINDING SITE FOR RESIDUE PEG A 234
04	AC4	SOFTWARE	HIS A:51 , PHE A:55 , GLY A:81 , ARG A:171	BINDING SITE FOR RESIDUE PEG A 235
05	AC5	SOFTWARE	ARG A:211 , U5P A:232 , HOH A:433 , HOH A:444 , ILE B:66 , ASN B:68	BINDING SITE FOR RESIDUE PGE A 236
06	AC6	SOFTWARE	ASP A:23 , ILE A:25 , ASP A:26 , PRO A:27 , LEU A:112 , ASP A:153 , LYS A:174 , GLU A:220 , HOH A:335 , HOH A:370 , HOH A:461 , HOH A:471	BINDING SITE FOR RESIDUE TRS A 237
07	AC7	SOFTWARE	ILE A:66 , HOH A:290 , HOH A:430 , ALA B:9 , ASP B:11 , LYS B:33 , THR B:120 , PRO B:178 , ARG B:181 , VAL B:208 , GLY B:210 , ARG B:211 , HOH B:266 , HOH B:320 , HOH B:376 , HOH B:381 , HOH B:397 , HOH B:429 , HOH B:433	BINDING SITE FOR RESIDUE U5P B 232
08	AC8	SOFTWARE	HIS B:51 , GLY B:54 , PHE B:55 , GLY B:81 , HOH B:313	BINDING SITE FOR RESIDUE PEG B 233
09	AC9	SOFTWARE	ALA A:201 , SER A:202 , HOH A:448 , SER B:163 , HOH B:399 , HOH B:406	BINDING SITE FOR RESIDUE PEG B 234
10	BC1	SOFTWARE	ALA B:78 , GLU B:79 , PRO B:105	BINDING SITE FOR RESIDUE PGE B 235

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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:222
 aligned with PYRF_VIBCH | Q9KQT7 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
           PYRF_VIBCH     2 NDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGSEQGDQRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
               SCOP domains d3uwqa_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhh....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeeee.....-------....hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uwq A   2 NDPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPA-------RRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 |     191       201       211       221         
                                                                                                                                                                                                               183     191

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with PYRF_VIBCH | Q9KQT7 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
           PYRF_VIBCH     3 DPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGSEQGDQRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
               SCOP domains d3uwqb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhh....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh...eeeee.......----.....hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uwq B   3 DPKVIVALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHKRGFSVFLDLKFHDIPNTCSKAVKAAAELGVWMVNVHASGGERMMAASREILEPYGKERPLLIGVTVLTSMESADLQGIGILSAPQDHVLRLATLTKNAGLDGVVCSAQEASLLKQHLGREFKLVTPGIRPAGS----QRRIMTPAQAIASGSDYLVIGRPITQAAHPEVVLEEINSSL 230
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  |    192       202       212       222        
                                                                                                                                                                                                                185  190

Legend:		→ Mismatch	(orange background)
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Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRF_VIBCH | Q9KQT7)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0004590	orotidine-5'-phosphate decarboxylase activity	Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	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.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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