2Z2B - JenaLib

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Title :   DELETION 107-116 MUTANT OF DIHYDROOROTASE FROM E. COLI

Authors :   M. Lee, M. J. Maher, J. M. Guss

Date :   17 May 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

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

Reference :   M. Lee, M. J. Maher, R. I. Christopherson, J. M. Guss
Kinetic And Structural Analysis Of Mutant Escherichia Coli Dihydroorotases: A Flexible Loop Stabilizes The Transition State
Biochemistry V. 46 10538 2007
PubMed-ID: 17711307 | Reference-DOI: 10.1021/BI701098E

Molecule 1 - DIHYDROOROTASE
	Chains	:	A
	EC Number	:	3.5.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBLUESCRIPT
	Expression System Strain	:	X7014A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYRC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DHOASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	KCX A:102 , HIS A:129 , HIS A:167 , ZN A:338 , HOH A:1346	BINDING SITE FOR RESIDUE ZN A 1337
2	AC2	SOFTWARE	HIS A:16 , HIS A:18 , KCX A:102 , ASP A:240 , ZN A:1337 , HOH A:1346	BINDING SITE FOR RESIDUE ZN A 338

(no "SS Bond" information available for 2Z2B)

Asymmetric Unit

No.	Residues
1	Ala A:46	-	Pro A:47
2	Leu A:212	-	Pro A:213

(no "SAP(SNP)/Variant" information available for 2Z2B)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_ECOLI	15-23	1	A:14-22
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_ECOLI	249-260	1	A:238-249

Biological Unit 1 (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
2	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_ECOLI	249-260	2	A:238-249

(no "Exon" information available for 2Z2B)

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:331
 aligned with PYRC_ECOLI | P05020 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:341
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346 
           PYRC_ECOLI     7 VLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d2z2ba_ A: Dihydroorotase                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2z2bA00 A:6-336 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---Amidohydro_1-2z2bA01 A:9-312                                                                      ----------                                                                                                                                                                                                              ------------------------ Pfam domains
         Sec.struct. author .eeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhh..eeeeee...----------.hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh...eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhh...eee.......hhhhh.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeeeeeee....ee....ee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z2b A   6 VLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPA----------TSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 336
                                    15        25        35        45        55        65        75        85        95      |105|        - |     115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335 
                                                                                                                          102-KCX        107

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

d2z2ba_

Asymmetric 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)

2z2bA00

A:6-336

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Escherichia coli (strain K12) (12)

Amidohydro_1-2z2bA01

A:9-312

Asymmetric Unit(hide GO term definitions)

Chain A (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 Unit
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	Ligands, Modified Residues, Ions
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Ala A:46 - Pro A:47	[ RasMol ]
		Leu A:212 - Pro A:213	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2z2b
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	PYRC_ECOLI \| P05020
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	3.5.2.3
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	PYRC_ECOLI \| P05020
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UniProtKB/Swiss-Prot
	PYRC_ECOLI \| P05020	:	1j79 1xge 2e25 2eg6 2eg7 2eg8 2z24 2z25 2z26 2z27 2z28 2z29 2z2a

1xge	WILD-TYPE DIHYDROOROTASE FROM E. COLI
2z24
2z25
2z26
2z27
2z28
2z29
2z2a

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Gene Ontology (10, 10)

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