2QCH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN OF HUMAN UMP SYNTHASE BOUND TO 5-IODO-UMP

Authors :   J. Wittmann, M. Rudolph

Date :   19 Jun 07 (Deposition) - 06 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Ump Synthase, Decarboxylase, Catalytic Proficiency, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. G. Wittmann, D. Heinrich, K. Gasow, A. Frey, U. Diederichsen, M. G. Rudolph
Structures Of The Human Orotidine-5'-Monophosphate Decarboxylase Support A Covalent Mechanism And Provide A Framework For Drug Design.
Structure V. 16 82 2008
PubMed-ID: 18184586 | Reference-DOI: 10.1016/J.STR.2007.10.020

Molecule 1 - URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE)
	Chains	:	A, B
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-30
	Expression System Strain	:	BL21 ROSETTA 2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	UMPS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	5IU	2	Mod. Residue	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	IOD	2	Ligand/Ion	IODIDE ION
3	UMP	2	Ligand/Ion	2'-DEOXYURIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	5IU A:1 , UMP A:2 , ASP A:312 , LYS A:314 , ASN A:341	BINDING SITE FOR RESIDUE IOD A 5
2	AC2	SOFTWARE	5IU B:3 , UMP B:4 , ASP B:312 , LYS B:314	BINDING SITE FOR RESIDUE IOD B 6
3	AC3	SOFTWARE	UMP A:2 , IOD A:5 , SER A:257 , ASP A:259 , LYS A:281 , HIS A:283 , LYS A:314 , MET A:371 , SER A:372 , PRO A:417 , GLN A:430 , TYR A:432 , GLY A:450 , ARG A:451 , HOH A:481 , HOH A:485 , ASP B:317 , ILE B:318 , THR B:321	BINDING SITE FOR RESIDUE 5IU A 1
4	AC4	SOFTWARE	5IU A:1 , IOD A:5 , SER A:257 , ASP A:259 , LYS A:281 , HIS A:283 , LYS A:314 , MET A:371 , SER A:372 , PRO A:417 , GLN A:430 , TYR A:432 , GLY A:450 , ARG A:451 , HOH A:481 , HOH A:485 , HOH A:507 , ASP B:317 , ILE B:318 , THR B:321	BINDING SITE FOR RESIDUE UMP A 2
5	AC5	SOFTWARE	ASP A:317 , THR A:321 , UMP B:4 , IOD B:6 , SER B:257 , ASP B:259 , LYS B:281 , HIS B:283 , LYS B:314 , ILE B:368 , MET B:371 , SER B:372 , PRO B:417 , GLN B:430 , TYR B:432 , VAL B:449 , GLY B:450 , ARG B:451 , HOH B:482 , HOH B:510	BINDING SITE FOR RESIDUE 5IU B 3
6	AC6	SOFTWARE	ASP A:317 , ILE A:318 , THR A:321 , 5IU B:3 , IOD B:6 , SER B:257 , ASP B:259 , LYS B:281 , HIS B:283 , LYS B:314 , MET B:371 , SER B:372 , PRO B:417 , GLN B:430 , TYR B:432 , GLY B:450 , ARG B:451 , HOH B:482 , HOH B:510	BINDING SITE FOR RESIDUE UMP B 4

(no "SS Bond" information available for 2QCH)

(no "Cis Peptide Bond" information available for 2QCH)

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006810	G	429	R	UMPS_HUMAN	Disease (ORAC1)	121917891	A/B	G	429	R
2	UniProt	VAR_020615	I	446	V	UMPS_HUMAN	Polymorphism	3772809	A/B	I	446	V

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	UMPS_HUMAN	309-322	2	A:309-322 B:309-322

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000232607	1a	ENSE00000823837	chr3:124449213-124449474	262	UMPS_HUMAN	1-52	52	0	-	-
1.3	ENST00000232607	3	ENSE00000776933	chr3:124453940-124454093	154	UMPS_HUMAN	53-104	52	0	-	-
1.5a	ENST00000232607	5a	ENSE00000776934	chr3:124456415-124457086	672	UMPS_HUMAN	104-328	225	2	A:224-328 B:224-328	105 105
1.7	ENST00000232607	7	ENSE00000823838	chr3:124458871-124459046	176	UMPS_HUMAN	328-386	59	2	A:328-386 B:328-386	59 59
1.8a	ENST00000232607	8a	ENSE00000823839	chr3:124460999-124461113	115	UMPS_HUMAN	387-425	39	2	A:387-425 B:387-425	39 39
1.9d	ENST00000232607	9d	ENSE00001382696	chr3:124462762-124464040	1279	UMPS_HUMAN	425-480	56	2	A:425-478 B:425-478	54 54

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:255
 aligned with UMPS_HUMAN | P11172 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:255
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473     
           UMPS_HUMAN   224 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRL 478
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qchA00 A:224-478 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhhh.eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh....eeeee...........eeee.......ee.....ee.hhhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------V-------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:224-328 UniProt: 104-328 [INCOMPLETE]                                                  ----------------------------------------------------------Exon 1.8a  PDB: A:387-425              ----------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:328-386 UniProt: 328-386                  --------------------------------------Exon 1.9d  PDB: A:425-478 UniProt: 425-480             Transcript 1 (2)
                 2qch A 224 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRL 478
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with UMPS_HUMAN | P11172 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:255
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473     
           UMPS_HUMAN   224 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRL 478
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qchB00 B:224-478 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh.eeee.hhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhh....eeeee...........eeee.................hhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------V-------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------OMPDECASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: B:224-328 UniProt: 104-328 [INCOMPLETE]                                                  ----------------------------------------------------------Exon 1.8a  PDB: B:387-425              ----------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:328-386 UniProt: 328-386                  --------------------------------------Exon 1.9d  PDB: B:425-478 UniProt: 425-480             Transcript 1 (2)
                 2qch B 224 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRL 478
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473

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 '\|'

(no "SCOP Domain" information available for 2QCH)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Human (Homo sapiens) (78)

1a	2qchA00	A:224-478
1b	2qchB00	B:224-478

(no "Pfam Domain" information available for 2QCH)

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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		5IU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IOD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qch)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2qch
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	UMPS_HUMAN \| P11172
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.1.23
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	258900
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	UMPS_HUMAN \| P11172
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (1, 2)

Exons (4, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (20, 20)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File