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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 5-CN-UMP
 
Authors :  Y. Liu, H. L. Tang, M. E. M. Avina, L. P. Kotra, E. F. Pai
Date :  05 Dec 07  (Deposition) - 18 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ump Synthase, C-Terminal Domain, Orotidine 5'-Monophosphate Decarboxylase, Human, 5-Cn-Ump, Disease Mutation, Glycosyltransferase, Lyase, Multifunctional Enzyme, Pyrimidine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Liu, H. L. Tang, M. E. M. Avina, L. P. Kotra, E. F. Pai
Crystal Structure Of Human Orotidine 5'-Monophosphate Decarboxylase Complexed With 5-Cn-Ump
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDINE 5'-MONOPHOSPHATE SYNTHASE
    ChainsA, B
    EC Number4.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUMPS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUMP SYNTHASE, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CNU2Ligand/Ion5-CYANO-URIDINE-5'-MONOPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:39 , GLU A:43BINDING SITE FOR RESIDUE SO4 A 3001
2AC2SOFTWARESER A:68 , ASP A:70 , LYS A:92 , HIS A:94 , ASP A:123 , ILE A:179 , MET A:182 , SER A:183 , ILE A:212 , PRO A:228 , GLN A:241 , TYR A:243 , GLY A:261 , ARG A:262 , HOH A:3002 , HOH A:3006 , HOH A:3074 , ASP B:128 , THR B:132BINDING SITE FOR RESIDUE CNU A 1000
3AC3SOFTWAREASP A:128 , ILE A:129 , THR A:132 , SER B:68 , ASP B:70 , LYS B:92 , HIS B:94 , ASP B:123 , ILE B:179 , MET B:182 , SER B:183 , ILE B:212 , PRO B:228 , GLN B:241 , TYR B:243 , GLY B:261 , ARG B:262 , HOH B:1002 , HOH B:1005 , HOH B:1015BINDING SITE FOR RESIDUE CNU B 1001
4AC4SOFTWARELYS A:53 , ALA A:113 , GLU A:117 , PHE A:118 , ASP A:149 , HOH A:3099BINDING SITE FOR RESIDUE GOL A 2000
5AC5SOFTWAREARG A:46 , HIS A:48 , PRO A:49 , SER A:205 , HOH A:3117BINDING SITE FOR RESIDUE GOL A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006810G429RUMPS_HUMANDisease (ORAC1)121917891A/BG240R
2UniProtVAR_020615I446VUMPS_HUMANPolymorphism3772809A/BI257V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPDECASEPS00156 Orotidine 5'-phosphate decarboxylase active site.UMPS_HUMAN309-322
 
  2A:120-133
B:120-133

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002326071aENSE00000823837chr3:124449213-124449474262UMPS_HUMAN1-52520--
1.3ENST000002326073ENSE00000776933chr3:124453940-124454093154UMPS_HUMAN53-104520--
1.5aENST000002326075aENSE00000776934chr3:124456415-124457086672UMPS_HUMAN104-3282252A:34-139
B:34-139
106
106
1.7ENST000002326077ENSE00000823838chr3:124458871-124459046176UMPS_HUMAN328-386592A:139-197
B:139-197
59
59
1.8aENST000002326078aENSE00000823839chr3:124460999-124461113115UMPS_HUMAN387-425392A:198-236
B:198-236
39
39
1.9dENST000002326079dENSE00001382696chr3:124462762-1244640401279UMPS_HUMAN425-480562A:236-290
B:236-290
55
55

(-) 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:257
 aligned with UMPS_HUMAN | P11172 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:257
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       
           UMPS_HUMAN   223 KELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 479
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bk0A00 A:34-290 Aldolase class I                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhh....eeeee...........eeee.......ee.....ee.hhhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------V--------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:34-139 UniProt: 104-328 [INCOMPLETE]                                                    ----------------------------------------------------------Exon 1.8a  PDB: A:198-236              ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:139-197 UniProt: 328-386                  --------------------------------------Exon 1.9d  PDB: A:236-290 UniProt: 425-480 [INCOMPLETE] Transcript 1 (2)
                 3bk0 A  34 KELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 290
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with UMPS_HUMAN | P11172 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:257
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       
           UMPS_HUMAN   223 KELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 479
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bk0B00 B:34-290 Aldolase class I                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhh...eeeee...........eeee.......ee.....ee.hhhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------V--------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: B:34-139 UniProt: 104-328 [INCOMPLETE]                                                    ----------------------------------------------------------Exon 1.8a  PDB: B:198-236              ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:139-197 UniProt: 328-386                  --------------------------------------Exon 1.9d  PDB: B:236-290 UniProt: 425-480 [INCOMPLETE] Transcript 1 (2)
                 3bk0 B  34 KELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 290
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       

   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)

(no "SCOP Domain" information available for 3BK0)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BK0)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UMPS_HUMAN | P11172)
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:0004588    orotate phosphoribosyltransferase activity    Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0006222    UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    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:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0046134    pyrimidine nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UMPS_HUMAN | P111722eaw 2jgy 2p1f 2qcc 2qcd 2qce 2qcf 2qcg 2qch 2qcl 2qcm 2qcn 2v30 2wns 3bgg 3bgj 3bvj 3dbp 3ewu 3eww 3ewx 3ewy 3ewz 3ex1 3ex2 3ex3 3ex4 3ex6 3g3d 3g3m 3l0k 3l0n 3mi2 3mo7 3mw7 4hib 4hkp

(-) Related Entries Specified in the PDB File

2eaw HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE)
2p1f HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE)
3bgg CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH BMP
3bgj CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COVALENTLY MODIFIED BY 6-IODO-UMP
3bvj CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH XMP