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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE O-CARBAMOYLTRANSFERASE TOBZ IN COMPLEX WITH CARBAMOYL PHOSPHATE

Authors :   C. Parthier, M. T. Stubbs, S. Goerlich, F. Jaenecke

Date :   09 Jan 12 (Deposition) - 25 Jan 12 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A

Keywords :   Antibiotic Biosynthesis, Substrate Assisted Catalysis, Substrate Channeling, Adenylation, Structural Enzymology, Enzyme Evolution, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Parthier, S. Gorlich, F. Jaenecke, C. Breithaupt, U. Brauer, U. Fandrich, D. Clausnitzer, U. F. Wehmeier, C. Bottcher, D. Scheel, M. T. Stubbs
The O-Carbamoyltransferase Tobz Catalyzes An Ancient Enzymatic Reaction.
Angew. Chem. Int. Ed. Engl. V. 51 4046 2012
PubMed-ID: 22383337 | Reference-DOI: 10.1002/ANIE.201108896

Molecule 1 - O-CARBAMOYLTRANSFERASE TOBZ
	Chains	:	A
	EC Number	:	2.1.3.-
	Engineered	:	YES
	Expression System	:	STREPTOMYCES LIVIDANS
	Expression System Plasmid	:	PUWL201PW
	Expression System Strain	:	TK24
	Expression System Taxid	:	457428
	Expression System Vector Type	:	PLASMID
	Gene	:	TACA, TOBZ
	Mutation	:	YES
	Organism Common	:	STREPTOMYCES TENEBRARIUS
	Organism Scientific	:	STREPTOALLOTEICHUS TENEBRARIUS
	Organism Taxid	:	1933
	Strain	:	DSM40770T

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CP	1	Ligand/Ion	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FE2	1	Ligand/Ion	FE (II) ION
4	K	2	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:418 , ALA A:419 , MET A:473 , ARG A:498 , ASN A:528 , THR A:529 , SER A:530 , HOH A:873 , HOH A:874 , HOH A:875 , HOH A:920 , HOH A:1044	BINDING SITE FOR RESIDUE CP A 601
2	AC2	SOFTWARE	HIS A:114 , HIS A:118 , ASP A:137 , ASP A:338 , HOH A:943	BINDING SITE FOR RESIDUE FE2 A 602
3	AC3	SOFTWARE	LEU A:322 , THR A:323 , ARG A:324 , VAL A:327	BINDING SITE FOR RESIDUE K A 603
4	AC4	SOFTWARE	THR A:565 , ASP A:567 , ARG A:569	BINDING SITE FOR RESIDUE K A 604
5	AC5	SOFTWARE	GLU A:369 , PHE A:370 , ALA A:409 , GLY A:411 , GLY A:560 , HOH A:966	BINDING SITE FOR RESIDUE EDO A 605

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

(no "Cis Peptide Bond" information available for 3VEO)

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

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

(no "Exon" information available for 3VEO)

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:571
 aligned with TOBZ_STRSD | Q70IY1 from UniProtKB/Swiss-Prot  Length:570

    Alignment length:571
                             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       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569 
           TOBZ_STRSD     - -MRVLGLNGWPRDFHDASAALLVDGRIAAFAEEERFTRKKHGYNTAPVQAAAFCLAQAGLTVDDLDAVAFGWDLPAMYRERLGGWPHSDSEALDILLPRDVFPRRTDPPLHFVQHHLAHAASAYYFSGEDRGAVLIVDGQGEEECVTLAHAEGGKITVLDTVPGAWSLGFFYEHVSEYTGLGGDNPGKLMGLAAHGTTVDETLSAFAFDSDGYRLNLIDPQARDPEDWDEYSVTERAWFAHLERIYRLPPNEFVRRYDPAKGRVVRDTRRDPYEYRDLAATAQAALERAVFGLADSVLARTGERTLFVAGGVGLNATMNGKLLTRSTVDKMFVPPVASDIGVSLGAAAAVAVELGDRIAPMGDTAAWGPEFSPDQVRAALDRTGLAYREPANLEREVAALIASGKVVGWAQGRGEVGPRALGQRSLLGSAHSPTMRDHINLRVKDREWWRPFAPSMLRSVSDQVLEVDADFPYMIMTTKVRAAYAERLPSVVHEDWSTRPQTVTEASNPRYHRMLTELGDLVGDPVCLNTSFNDRGEPIVSSPADALLTFSRLPIDALAVGPYLVTKDLRH 570
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeeee..eeeeeeehhhhhh........hhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhh.....hhhhhhhhhh............eee.hhhhhhhhhhhh.....eeeeeee......eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhh.....hhhhhhhhhh...........eeee..eeee..............hhhhhhhhhhhhhhhhh......eeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh.................hhhhhhhhhhhhh.......hhhhhhhhhhhh...eeee.............eeeeee....hhhhhhhhh...........eeeehhhhhhhh............ee.hhhhh...........ee..eee....hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhh...eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3veo A   0 HMRVLGLNGWPRDFHDASAALLVDGRIAAFAEEERLTRKKHGYNTAPVQAAAFCLAQAGLTVDDLDAVAFGWDLPAMYRERLGGWPHSDSEALDILLPRDVFPRRTDPPLHFVQHHLAHAASAYYFSGEDRGAVLIVDGQGEEECVTLAHAEGGKITVLDTVPGAWSLGFFYEHVSEYTGLGGDNPGKLMGLAAHGTTVDETLSAFAFDSDGYRLNLIDPQARDPEDWDEYSVTERAWFAHLERIYRLPPNEFVRRYDPAKGRVVRDTRRDPYEYRDLAATAQAALERAVFGLADSVLARTGERTLFVAGGVGLNATMNGKLLTRSTVDKMFVPPVASDIGVSLGAAAAVAVELGDRIAPMGDTAAWGPEFSPDQVRAALDRTGLAYREPANLEREVAALIASGKVVGWAQGRGEVGPRALGQRSLLGSAHSPTMRDHINLRVKDREWWRPFAPSMLRSVSDQVLEVDADFPYMIMTTKVRAAYAERLPSVVHEDWSTRPQTVTEASNPRYHRMLTELGDLVGDPVCLNTSFNDRGEPIVSSPADALLTFSRLPIDALAVGPYLVTKDLRH 570
                                     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       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569

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 3VEO)

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

(no "Pfam Domain" information available for 3VEO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TOBZ_STRSD | Q70IY1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:1901133	kanamycin biosynthetic process	The chemical reactions and pathways resulting in the formation of kanamycin.
	GO:1901121	tobramycin biosynthetic process	The chemical reactions and pathways resulting in the formation of tobramycin.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3veo)

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Access by PDB/NDB ID
	3veo
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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Access by UniProt ID/Accession number
	TOBZ_STRSD \| Q70IY1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	2.1.3.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	TOBZ_STRSD \| Q70IY1
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UniProtKB/Swiss-Prot
	TOBZ_STRSD \| Q70IY1	:	3ven 3ver 3ves 3vet 3vew 3vex 3vez 3vf2 3vf4

3ven	TOBZ
3ver	TOBZ IN COMPLEX WITH CARBAMOYL ADENYLATE INTERMEDIATE
3ves	TOBZ IN COMPLEX WITH AMPCPP AND CARBAMOYL PHOSPHATE
3vet	TOBZ IN COMPLEX WITH TOBRAMYCIN, CARBAMOYL PHOSPHATE AND ADP
3vew	TOBZ IN COMPLEX WITH ADP
3vex	TOBZ H14N VARIANT IN COMPLEX WITH CARBAMOYL ADENYLATE INTERMEDIATE
3vez	TOBZ K443A VARIANT IN COMPLEX WITH ATP, ADP AND CARBAMOYL PHOSPHATE
3vf2	TOBZ M473I VARIANT IN COMPLEX WITH CARBAMOYL PHOSPHATE AND ADP
3vf4	TOBZ S530A VARIANT IN COMPLEX WITH CARBAMOYL PHOSPHATE AND ADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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