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Asym./Biol. Unit (Jmol Viewer)

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Title :   HIS257ALA MUTANT OF DIHYDROOROTASE FROM E. COLI

Authors :   K. E. Ernberg, J. M. Guss, M. Lee, M. J. Maher

Date :   13 Apr 10 (Deposition) - 02 Mar 11 (Release) - 02 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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

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

Reference :   K. E. Ernberg, M. Lee, R. I. Christopherson, M. J. Maher, J. M. Guss
His257Ala Mutant Of Dihydroorotase From E. Coli
To Be Published
PubMed: search

Molecule 1 - DIHYDROOROTASE
	Chains	:	A, B
	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	:	ECOLC_2538, PYRC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI ATCC 8739
	Organism Taxid	:	481805
	Strain	:	ATCC 8739 / DSM 1576 / CROOKS
	Synonym	:	DHOASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 9)

No.	Name	Count	Type	Full Name
1	CP	1	Ligand/Ion	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2	DOR	1	Ligand/Ion	(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NCD	1	Ligand/Ion	N-CARBAMOYL-L-ASPARTATE
5	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	KCX A:102 , HIS A:139 , HIS A:177 , ZN A:401 , HOH A:453 , DOR A:1410	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	HIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:400 , HOH A:453	BINDING SITE FOR RESIDUE ZN A 401
3	AC3	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:400 , HOH A:453 , HOH A:496	BINDING SITE FOR RESIDUE DOR A 1410
4	AC4	SOFTWARE	KCX B:102 , HIS B:139 , HIS B:177 , NCD B:2410	BINDING SITE FOR RESIDUE ZN B 400
5	AC5	SOFTWARE	HIS B:16 , HIS B:18 , KCX B:102 , ASP B:250 , NCD B:2410	BINDING SITE FOR RESIDUE ZN B 401
6	AC6	SOFTWARE	HIS B:18 , ARG B:20 , ASN B:44 , KCX B:102 , THR B:109 , THR B:110 , HIS B:139 , HIS B:177 , 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	BINDING SITE FOR RESIDUE NCD B 2410
7	AC7	SOFTWARE	PHE A:150 , ARG A:207 , ARG A:227 , HOH A:592 , PHE B:150 , ARG B:207 , ARG B:227 , HOH B:352 , HOH B:517	BINDING SITE FOR RESIDUE CP B 348

(no "SS Bond" information available for 3MJM)

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 3MJM)

Asymmetric/Biological Unit (2, 4)

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

(no "Exon" information available for 3MJM)

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:344
 aligned with PYRC_ECOLC | B1IV40 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:344
                                    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    
           PYRC_ECOLC     4 PSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d3mjma_ A: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjm A   3 PSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARARKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 346
                                    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       312       322       332       342    
                                                                                                                             102-KCX

Chain B from PDB  Type:PROTEIN  Length:343
 aligned with PYRC_ECOLC | B1IV40 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_ECOLC     5 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 347
               SCOP domains d3mjmb_ B: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Amidohydro_1-3mjmB01 B:9-322                                                                                                                                                                                                                                                                                              ------------------------ Pfam domains (1)
           Pfam domains (2) -----Amidohydro_1-3mjmB02 B:9-322                                                                                                                                                                                                                                                                                              ------------------------ Pfam domains (2)
         Sec.struct. author ..eeeee...eeee...hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhh....eeeeehhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhh....eee.......hhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee....ee....ee.......ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DIHYDROOR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjm B   4 SQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAkLYPANATTNSSHGVTSVDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARARKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVK 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

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(

)

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: automated matches (2)

Escherichia coli [TaxId: 481805] (1)

1a	d3mjma_	A:
1b	d3mjmb_	B:

(no "CATH Domain" information available for 3MJM)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) (1)

1a	Amidohydro_1-3mjmB01	B:9-322
1b	Amidohydro_1-3mjmB02	B:9-322

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRC_ECOLC | B1IV40)

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: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.

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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	3mjm
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	3.5.2.3
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(no "Entries Sharing at Least One Protein Chain" available for 3MJM)

1xge	WILDTYPE DHOASE FROM E. COLI
2z24	T110S MUTANT DHOASE
2z25	T110V MUTANT DHOASE
2z26	T110A MUTANT DHOASE
2z27	T109S MUTANT DHOASE
2z28	T109V MUTANT DHOASE
2z29	T109A MUTANT DHOASE
2z2a	T109G MUTANT DHOASE
2z2b	DEL 107-116 MUTANT DHOASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 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)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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