1XRT - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF A NOVEL, LATENT DIHYDROOROTASE FROM AQUIFEX AEOLICUS AT 1.7 A RESOLUTION

Authors :   P. D. Martin, C. Purcarea, P. Zhang, A. Vaishnav, S. Sadecki, H. I. Guy-E D. R. Evans, B. F. Edwards

Date :   15 Oct 04 (Deposition) - 05 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

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

Keywords :   Dihydroorotase, Amidohydrolase, Metalloenzyme, Pyrimidine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. D. Martin, C. Purcarea, P. Zhang, A. Vaishnav, S. Sadecki, H. I. Guy-Evans, D. R. Evans, B. F. Edwards
The Crystal Structure Of A Novel, Latent Dihydroorotase Fro Aquifex Aeolicus At 1. 7A Resolution
J. Mol. Biol. V. 348 535 2005
PubMed-ID: 15826652 | Reference-DOI: 10.1016/J.JMB.2005.03.015

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	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	DHOASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:61 , HIS A:63 , ASP A:153 , CYS A:181 , ASP A:305	BINDING SITE FOR RESIDUE ZN A 1423
2	AC2	SOFTWARE	HIS B:61 , HIS B:63 , ASP B:153 , CYS B:181 , ASP B:305	BINDING SITE FOR RESIDUE ZN B 1424

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

Asymmetric Unit

No.	Residues
1	Asp A:66	-	Pro A:67
2	Asn A:97	-	Pro A:98
3	Asp B:66	-	Pro B:67
4	Asn B:97	-	Pro B:98

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	2	A:59-67 B:59-67
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	2	A:303-311 B:303-311

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	1	A:59-67 -
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	1	A:303-311 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	1	- B:59-67
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	1	- B:303-311

(no "Exon" information available for 1XRT)

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:369
 aligned with PYRC_AQUAE | O66990 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420  
           PYRC_AQUAE     1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
               SCOP domains d1xrta1 A:1-55,A:366-422 Two-domain dihydroorotase     d1xrta2 A:56-365 Two-domain dihydroorotase                                                                                                                                                                                                                                                                            d1xrta1 A:1-55,A:366-422 Two-domain dihydroorotase        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeehhhheeee.eeeee..eeeeee.......eeeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee....hhhhh.....hhhhhhhhh............hhhhhhhhhhhhhhhh.eeee..hhhhhh.--------------------hhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeeeehhhhhh----------------------.hhhhhhhhhhh....ee.........-----------...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............eeeeeeeeeee..................eeeeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------DIHYDROOR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xrt A   1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAY--------------------AEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLL----------------------EDRLALIEGVKRGIIDCFATDHAPHQT-----------GIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -         -       210       220       230       240       250       260 |       -         -    |  290       300       310|        -  |    330       340       350       360       370       380       390       400       410       420  
                                                                                                                                                                                                                     188                  209                                                  262                    285                       311         323

Chain B from PDB  Type:PROTEIN  Length:369
 aligned with PYRC_AQUAE | O66990 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:423
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419   
           PYRC_AQUAE     - -MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
               SCOP domains d1xrtb1 B:0-55,B:366-422 Two-domain dihydroorotase      d1xrtb2 B:56-365 Two-domain dihydroorotase                                                                                                                                                                                                                                                                            d1xrtb1 B:0-55,B:366-422 Two-domain dihydroorotase        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------Amidohydro_4-1xrtB01 B:47-376                                                                                                                                                                                                                                                                                                             ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Amidohydro_4-1xrtB02 B:47-376                                                                                                                                                                                                                                                                                                             ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee..eeeehhhheeee.eeeee..eeeeee.......eeeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee....hhhhh.....hhhhhhhhh............hhhhhhhhhhhhhhhh..eee..hhhhh.--------------------hhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeehhhhhh------------------------hhhhhhhhhh....ee.........----------....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............eeeeeeeeeee..................eeeeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------DIHYDROOR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xrt B   0 WMLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLA--------------------EAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLL------------------------RLALIEGVKRGIIDCFATDHAPHQT----------PGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       | -         -       209       219       229       239       249       259  |      -         -       289       299       309 |       -  |    329       339       349       359       369       379       389       399       409       419   
                                                                                                                                                                                                                     187                  208                                                   262                      287                     311        322

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 "CATH Domain" information available for 1XRT)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_4 (8)

Aquifex aeolicus (2)

1a	Amidohydro_4-1xrtB01	B:47-376
1b	Amidohydro_4-1xrtB02	B:47-376

Asymmetric Unit(hide GO term definitions)

Chain A,B (PYRC_AQUAE | O66990)

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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	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: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.

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	Cis Peptide Bonds
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		Asp A:66 - Pro A:67	[ RasMol ]
		Asp B:66 - Pro B:67	[ RasMol ]

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	1xrt
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	3.5.2.3
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	PYRC_AQUAE \| O66990	:	1xrf 3d6n 4bjh

1xrf	THE CRYSTAL STRUCTURE OF A NOVEL, LATENT DIHYDROOROTASE FROM AQUIFEX AEOLICUS AT 1.7 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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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Related Entries Specified in the PDB File