1J79 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   MOLECULAR STRUCTURE OF DIHYDROOROTASE: A PARADIGM FOR CATALYSIS THROUGH THE USE OF A BINUCLEAR METAL CENTER

Authors :   J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden

Date :   16 May 01 (Deposition) - 20 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Tim Barrel, Metalloenzyme, Pyrimidine Biosynthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden
Molecular Structure Of Dihydroorotase: A Paradigm For Catalysis Through The Use Of A Binuclear Metal Center.
Biochemistry V. 40 6989 2001
PubMed-ID: 11401542 | Reference-DOI: 10.1021/BI010682I
(for further references see the PDB file header)

Molecule 1 - DIHYDROOROTASE
	Chains	:	A, B
	EC Number	:	3.5.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PYRC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DHOASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	NCD	2	Ligand/Ion	N-CARBAMOYL-L-ASPARTATE
3	ORO	1	Ligand/Ion	OROTIC ACID
4	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:401 , HOH A:1407	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	KCX A:102 , HIS A:139 , HIS A:177 , ZN A:400 , ORO A:410 , HOH A:1407	BINDING SITE FOR RESIDUE ZN A 401
3	AC3	SOFTWARE	HIS B:16 , HIS B:18 , KCX B:102 , ASP B:250 , NCD B:411	BINDING SITE FOR RESIDUE ZN B 400
4	AC4	SOFTWARE	KCX B:102 , HIS B:139 , HIS B:177 , NCD B:411	BINDING SITE FOR RESIDUE ZN B 401
5	AC5	SOFTWARE	HIS A:18 , ARG A:20 , ASN A:44 , HIS A:139 , CYS A:221 , LEU A:222 , ASP A:250 , ALA A:252 , HIS A:254 , ALA A:266 , GLY A:267 , ZN A:401 , HOH A:1160 , HOH A:1407	BINDING SITE FOR RESIDUE ORO A 410
6	AC6	SOFTWARE	HIS B:18 , ARG B:20 , ASN B:44 , KCX B:102 , HIS B:139 , CYS B:221 , LEU B:222 , ASP B:250 , ALA B:252 , HIS B:254 , ALA B:266 , GLY B:267 , ZN B:400 , ZN B:401 , HOH B:1485	BINDING SITE FOR RESIDUE NCD B 411
7	AC7	SOFTWARE	ASN A:208 , HIS A:209 , VAL A:212 , HOH A:1110 , HOH A:1446 , ALA B:145 , ARG B:152	BINDING SITE FOR RESIDUE NCD A 950

(no "SS Bond" information available for 1J79)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:46	-	Pro A:47
2	Leu A:222	-	Pro A:223
3	Ala B:46	-	Pro B:47
4	Leu B:222	-	Pro B:223

(no "SAP(SNP)/Variant" information available for 1J79)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_ECOLI	15-23	2	A:14-22 B:14-22
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_ECOLI	249-260	2	A:248-259 B:248-259

(no "Exon" information available for 1J79)

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:343
 aligned with PYRC_ECOLI | P05020 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:343
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344   
           PYRC_ECOLI     5 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d1j79a_ A: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j79A00 A:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhh..eee..................hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhh...eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j79 A   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAPHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFQRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    13        23        33        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       293       303       313       323       333       343   
                                                                                                                            102-KCX

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with PYRC_ECOLI | P05020 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:343
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344   
           PYRC_ECOLI     5 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d1j79b_ B: Dihydroorotase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j79B00 B:4-346 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhh..eee........----.....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j79 B   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAPHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANA----SHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFQRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    13        23        33        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       293       303       313       323       333       343   
                                                                                                                            102-KCX08  113

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: Dihydroorotase (16)

Protein domain: Dihydroorotase (14)

Escherichia coli [TaxId: 562] (14)

1a	d1j79a_	A:
1b	d1j79b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Escherichia coli. Organism_taxid: 562. (27)

1a	1j79B00	B:4-346
1b	1j79A00	A:4-346

(no "Pfam Domain" information available for 1J79)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRC_ECOLI | P05020)

molecular function
	GO:0004151	dihydroorotase activity	Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0019856	pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:46 - Pro A:47	[ RasMol ]
		Ala B:46 - Pro B:47	[ RasMol ]
		Leu A:222 - Pro A:223	[ RasMol ]
		Leu B:222 - Pro B:223	[ RasMol ]

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	1j79
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	PYRC_ECOLI \| P05020	:	1xge 2e25 2eg6 2eg7 2eg8 2z24 2z25 2z26 2z27 2z28 2z29 2z2a 2z2b

(no "Related Entries Specified in the PDB File" available for 1J79)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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