3L04 - JenaLib

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Title :   CRYSTAL STRUCTURE OF N-ACETYL-L-ORNITHINE TRANSCARBAMYLASE E92P MUTANT COMPLEXED WITH CARBAMYL PHOSPHATE AND N-SUCCINYL-L-NORVALINE

Authors :   D. Shi, X. Yu, N. M. Allewell, M. Tuchman

Date :   09 Dec 09 (Deposition) - 31 Mar 10 (Release) - 31 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Transcarbamylase, Amino-Acid Biosynthesis, Arginine Biosynthesis, Cytoplasm, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Shi, X. Yu, J. Cabrera-Luque, T. Y. Chen, L. Roth, H. Morizono, N. M. Allewell, M. Tuchman
A Single Mutation In The Active Site Swaps The Substrate Specificity Of N-Acetyl-L-Ornithine Transcarbamylase And N-Succinyl-L-Ornithine Transcarbamylase.
Protein Sci. V. 16 1689 2007
PubMed-ID: 17600144 | Reference-DOI: 10.1110/PS.072919907

Molecule 1 - N-ACETYLORNITHINE CARBAMOYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.3.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ARGF, ARGF', XCC2249
	Mutation	:	YES
	Organism Scientific	:	XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
	Organism Taxid	:	190485
	Strain	:	ATCC 33913
	Synonym	:	AOTCASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CP	1	Ligand/Ion	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	SN0	1	Ligand/Ion	N-(3-CARBOXYPROPANOYL)-L-NORVALINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	CP	-1	Ligand/Ion	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2	KCX	3	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	SN0	3	Ligand/Ion	N-(3-CARBOXYPROPANOYL)-L-NORVALINE
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:77 , PRO A:92 , GLU A:144 , HIS A:180 , ASN A:185 , LYS A:252 , CYS A:294 , LEU A:295 , ARG A:298 , HOH A:340 , CP A:346 , HOH A:358 , HOH A:367 , HOH A:370 , HOH A:383 , HOH A:400	BINDING SITE FOR RESIDUE SN0 A 345
2	AC2	SOFTWARE	SER A:49 , MET A:50 , ARG A:51 , THR A:52 , TRP A:77 , ARG A:112 , HIS A:148 , GLN A:151 , CYS A:294 , LEU A:295 , ARG A:322 , SN0 A:345	BINDING SITE FOR RESIDUE CP A 346
3	AC3	SOFTWARE	PHE A:61 , HIS A:66 , HOH A:364	BINDING SITE FOR RESIDUE SO4 A 350

(no "SS Bond" information available for 3L04)

Asymmetric Unit

No.	Residues
1	Leu A:295	-	Pro A:296

(no "SAP(SNP)/Variant" information available for 3L04)

(no "PROSITE Motif" information available for 3L04)

(no "Exon" information available for 3L04)

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:332
 aligned with AOTC_XANCP | Q8P8J2 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:332
                                    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  
           AOTC_XANCP     3 LKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3l04A01 A:3-150,A:322-334  [code=3.40.50.1370, no name defined]                                                                                     3l04A02 A:151-321  [code=3.40.50.1370, no name defined]                                                                                                                    3l04A01       CATH domains
               Pfam domains -OTCace_N-3l04A02 A:4-162                                                                                                                                       ------OTCace-3l04A01 A:169-333                                                                                                                                             - Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee........ee............eehhhhhhhhhhhh.eeeee......hhhhhh.hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhh.......eeeeee........hhhhhhhhhhhhhh..eeeee..hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeeee...hhhhh....hhhhhhhhhhhhh.hhhhhhh....eee...........hhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l04 A   3 LKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTPEHIAEVARVLGRYVDLIGVRAFPKFVDWSKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRNVkATDAVMDSPNCIAIDEAENRLHVQKAIMAALV 334
                                    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  
                                                                                                                                                                                                                                                                                                                                     302-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 '\|'

(no "SCOP Domain" information available for 3L04)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1370, no name defined] (91)

Campestris (Xanthomonas campestris pv) (9)

1a	3l04A01	A:3-150,A:322-334
1b	3l04A02	A:151-321

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: OTCace] (48)

Family: OTCace (48)

Xanthomonas campestris pv. campestris (13)

OTCace-3l04A01

A:169-333

Clan: no clan defined [family: OTCace_N] (48)

Family: OTCace_N (48)

Xanthomonas campestris pv. campestris (13)

OTCace_N-3l04A02

A:4-162

Asymmetric Unit(hide GO term definitions)

Chain A (AOTC_XANCP | Q8P8J2)

molecular function
	GO:0043857	N-acetylornithine carbamoyltransferase activity	Catalysis of the reaction: N(2)-acetyl-L-ornithine + carbamoyl phosphate = N(2)-acetyl-L-citrulline + H(+) + phosphate.
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004070	aspartate carbamoyltransferase activity	Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	GO:0004585	ornithine carbamoyltransferase activity	Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	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:0006526	arginine biosynthetic process	The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0042450	arginine biosynthetic process via ornithine	The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0000050	urea cycle	The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
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
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	Ligands, Modified Residues, Ions
		CP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SN0	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Leu A:295 - Pro A:296	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3l04
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	2.1.3.9
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UniProtKB/Swiss-Prot
	AOTC_XANCP \| Q8P8J2	:	3kzc 3kzk 3kzm 3kzn 3kzo 3l02 3l05 3l06 3m4j 3m4n 3m5c 3m5d

2fg7	THE HOMOLOG PROTEIN FROM B. FRAGILIS COMPLEXED WITH CARBAMYL PHOSPHATE AND N-SUCCINYL-L-NORVALINE
3kzc	THE SAME PROTEIN COMPLEXED WITH SULFATE
3kzk	THE SAME PROTEIN COMPLEXED WITH SULFATE AND N-ACETYL-L- CITRULLINE
3kzm	THE SAME PROTEIN COMPLEXED WITH CARBAMYL PHOSPHATE
3kzn	THE SAME PROTEIN COMPLEXED WITH CARBAMYL PHOSPHATE
3kzo	THE SAME PROTEIN COMPLEXED WITH CARBAMYL PHOSPHATE AND N- ACETYL-L-NORVALINE
3l02	THE E92A MUTANT OF THE SAME PROTEIN COMPLEXED WITH CARBAMYL PHOSPHATE AND N-SUCCINYL-L-NORVALINE
3l05	THE E92S MUTANT OF THE SAME PROTEIN COMPLEXED WITH CARBAMYL PHOSPHATE AND N-SUCCINYL-L-NORVALINE
3l06	THE E92V MUTANT COMPLEXED WITH CARBAMYL PHOSPHATE AND N- SUCCINYL-L-NORVALINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (2, 2)

Gene Ontology (13, 13)

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