1EP1 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B

Authors :   P. Rowland, S. Norager, K. F. Jensen, S. Larsen

Date :   27 Mar 00 (Deposition) - 17 Jan 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Heterotetramer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Rowland, S. Norager, K. F. Jensen, S. Larsen
Structure Of Dihydroorotate Dehydrogenase B: Electron Transfer Between Two Flavin Groups Bridged By An Iron-Sulphur Cluster.
Structure Fold. Des. V. 8 1227 2000
PubMed-ID: 11188687 | Reference-DOI: 10.1016/S0969-2126(00)00530-X

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
	Chains	:	A
	EC Number	:	1.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358

Molecule 2 - DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
	Chains	:	B
	EC Number	:	1.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:23 , SER A:24 , GLY A:25 , CYS A:26 , ALA A:49 , ASN A:72 , ASN A:104 , ASN A:132 , LYS A:170 , ILE A:196 , ASN A:197 , THR A:198 , SER A:221 , GLY A:222 , MET A:247 , GLY A:248 , GLY A:249 , GLY A:270 , THR A:271 , HOH A:1001 , HOH A:1010 , HOH A:1088	BINDING SITE FOR RESIDUE FMN A 501
2	AC2	SOFTWARE	GLU A:65 , LEU B:51 , ARG B:53 , PRO B:54 , ILE B:55 , SER B:56 , LEU B:70 , TYR B:71 , ARG B:72 , THR B:78 , GLY B:79 , THR B:80 , ILE B:120 , GLU B:221 , SER B:222 , ARG B:223 , MET B:224 , HOH B:1051 , HOH B:1054 , HOH B:1063 , HOH B:1073 , HOH B:1078 , HOH B:1190	BINDING SITE FOR RESIDUE FAD B 502
3	AC3	SOFTWARE	MET B:224 , ALA B:225 , CYS B:226 , GLY B:227 , GLY B:229 , CYS B:231 , TYR B:232 , CYS B:234 , CYS B:249	BINDING SITE FOR RESIDUE FES B 503

(no "SS Bond" information available for 1EP1)

Asymmetric Unit

No.	Residues
1	Thr A:60	-	Pro A:61
2	Met A:195	-	Ile A:196
3	Gly B:96	-	Pro B:97
4	Gly B:252	-	Pro B:253

(no "SAP(SNP)/Variant" information available for 1EP1)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	PYRK_LACLM	3-104	1	B:3-104
2	DHODEHASE_1	PS00911	Dihydroorotate dehydrogenase signature 1.	PYRDB_LACLM	43-62	1	A:43-62
3	DHODEHASE_2	PS00912	Dihydroorotate dehydrogenase signature 2.	PYRDB_LACLM	244-264	1	A:244-264

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	PYRK_LACLM	3-104	2	B:3-104
2	DHODEHASE_1	PS00911	Dihydroorotate dehydrogenase signature 1.	PYRDB_LACLM	43-62	2	A:43-62
3	DHODEHASE_2	PS00912	Dihydroorotate dehydrogenase signature 2.	PYRDB_LACLM	244-264	2	A:244-264

(no "Exon" information available for 1EP1)

Asymmetric 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:309
 aligned with PYRDB_LACLM | P54322 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:309
                                    12        22        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         
          PYRDB_LACLM     3 ENNRLSVKLPGLDLKNPIIPASGCFGFGEEYAKYYDLNKLGSIMVKATTLHPRFGNPTPRVAETASGMLNAIGLQNPGLEVIMTEKLPWLNENFPELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGTDPEVAAALVKACKAVSKVPLYVKLSPNVTDIVPIAKAVEAAGADGLTMINTLMGVRFDLKTRQPILANITGGLSGPAIKPVALKLIHQVAQVVDIPIIGMGGVANAQDVLEMYMAGASAVAVGTANFADPFVCPKIIDKLPELMDQYRIESLESLIQEVKEGKK 311
               SCOP domains d1ep1a_ A: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ep1A00 A:3-311 Aldolase class I                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheee..eee...eee.......hhhhhh..hhhhh..eeeeee............eeee..eeee.......hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeeeee...ee.....ee...hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh...eeee...eee..ee....ee......eeeehhhhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------DHODEHASE_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ----------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ep1 A   3 ENNRLSVKLPGLDLKNPIIPASGCFGFGEEYAKYYDLNKLGSIMVKATTLHPRFGNPTPRVAETASGMLNAIGLQNPGLEVIMTEKLPWLNENFPELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGTDPEVAAALVKACKAVSKVPLYVKLSPNVTDIVPIAKAVEAAGADGLTMINTLMGVRFDLKTRQPILANITGGLSGPAIKPVALKLIHQVAQDVDIPIIGMGGVANAQDVLEMYMAGASAVAVGTANFADPFVCPKIIDKLPELMDQYRIESLESLIQEVKEGKK 311
                                    12        22        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

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with PYRK_LACLM | P56968 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                    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 
           PYRK_LACLM     2 SQLQEMMTVVSQREVAYNIFEMVLKGTLVDEMDLPGQFLHLAVPNGAMLLRRPISISSWDKRAKTCTILYRIGDETTGTYKLSKLESGAKVDVMGPLGNGFPVAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASENVKILENEFSNLKNVTLKIATDDGSYGTKGHVGMLMNEIDFEVDALYTCGAPAMLKAVAKKYDQLERLYISMESRMACGIGACYACVEHDKEDESHALKVCEDGPVFLGKQLSL 262
               SCOP domains d1ep1b1 B:2-102 Dihydroorotate dehydrogenase B, PyrK subunit                                         d1ep1b2 B:103-262 Dihydroorotate dehydrogenase B, PyrK subunit                                                                                                   SCOP domains
               CATH domains 1ep1B01 B:2-100 Translation factors                                                                ---1ep1B02 B:104-220 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                1ep1B03 B:221-262                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee..eeeeeee.hhhhhh.....eeee..........eeee..eee....eeeeeee.....hhhhhhh......eeeeeeee..............eeeeee..hhhhhhhhhhhhhh....eeeeeeeee.hhh.hhhhhhh...eeeeeeeeee...ee.hhhhhhhhh.....eeeee.hhhhhhhhhhhh....eeeee...............eee.......eee......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FAD_FR  PDB: B:3-104 UniProt: 3-104                                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ep1 B   2 SQLQEMMTVVSQREVAYNIFEMVLKGTLVDEMDLPGQFLHLAVPNGAMLLRRPISISSWDKRAKTCTILYRIGDETTGTYKLSKLESGAKVDVMGPLGNGFPVAEVTSTDKILIIGGGIGVPPLYELAKQLEKTGCQMTILLGFASENVKILENEFSNLKNVTLKIATDDGSYGTKGHVGMLMNEIDFEVDALYTCGAPAMLKAVAKKYDQLERLYISMESRMACGIGACYACVEHDKEDESHALKVCEDGPVFLGKQLSL 262
                                    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

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 "Pfam Domain" information available for 1EP1)

Asymmetric Unit(hide GO term definitions)

Chain A (PYRDB_LACLM | P54322)

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:0004152	dihydroorotate dehydrogenase activity	Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
	GO:0004589	orotate reductase (NADH) activity	Catalysis of the reaction: (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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.

Chain B (PYRK_LACLM | P56968)

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:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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.

Asymmetric 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
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly B:252 - Pro B:253	[ RasMol ]
		Gly B:96 - Pro B:97	[ RasMol ]
		Met A:195 - Ile A:196	[ RasMol ]
		Thr A:60 - Pro A:61	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	1ep1
		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
	PYRDB_LACLM \| P54322
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PYRK_LACLM \| P56968
		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)
	1.3.3.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		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
	PYRDB_LACLM \| P54322
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	PYRK_LACLM \| P56968
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PYRDB_LACLM \| P54322	:	1ep2 1ep3
	PYRK_LACLM \| P56968	:	1ep2 1ep3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (4, 4)

Pfam Domains (0, 0)

Gene Ontology (17, 23)

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