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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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

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 :   2.34

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
	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 (3, 4)

No.	Name	Count	Type	Full Name
1	CA0	2	Ligand/Ion	5'-O-[(S)-(CARBAMOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE
2	FE2	1	Ligand/Ion	FE (II) ION
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:114 , HIS A:118 , ASP A:137 , ASP A:338 , CA0 A:604	BINDING SITE FOR RESIDUE FE2 A 601
2	AC2	SOFTWARE	LEU A:322 , THR A:323 , ARG A:324 , VAL A:327	BINDING SITE FOR RESIDUE NA A 602
3	AC3	SOFTWARE	ARG A:418 , ALA A:419 , ARG A:445 , ARG A:449 , PRO A:450 , PHE A:451 , MET A:473 , THR A:476 , HIS A:492 , SER A:496 , THR A:497 , ARG A:498 , ASN A:528 , THR A:529 , SER A:530 , HOH A:715 , HOH A:806 , HOH A:996	BINDING SITE FOR RESIDUE CA0 A 603
4	AC4	SOFTWARE	HIS A:14 , TRP A:71 , HIS A:114 , HIS A:118 , ASP A:137 , GLY A:138 , GLN A:139 , GLY A:168 , PHE A:169 , TYR A:171 , GLU A:172 , PRO A:185 , GLY A:310 , VAL A:311 , ASN A:314 , SER A:337 , ASP A:338 , FE2 A:601 , HOH A:790 , HOH A:833	BINDING SITE FOR RESIDUE CA0 A 604

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

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

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

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

(no "Exon" information available for 3VER)

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
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Chain A from PDB  Type:PROTEIN  Length:566
 aligned with TOBZ_STRSD | Q70IY1 from UniProtKB/Swiss-Prot  Length:570

    Alignment length:566
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560      
           TOBZ_STRSD     1 MRVLGLNGWPRDFHDASAALLVDGRIAAFAEEERFTRKKHGYNTAPVQAAAFCLAQAGLTVDDLDAVAFGWDLPAMYRERLGGWPHSDSEALDILLPRDVFPRRTDPPLHFVQHHLAHAASAYYFSGEDRGAVLIVDGQGEEECVTLAHAEGGKITVLDTVPGAWSLGFFYEHVSEYTGLGGDNPGKLMGLAAHGTTVDETLSAFAFDSDGYRLNLIDPQARDPEDWDEYSVTERAWFAHLERIYRLPPNEFVRRYDPAKGRVVRDTRRDPYEYRDLAATAQAALERAVFGLADSVLARTGERTLFVAGGVGLNATMNGKLLTRSTVDKMFVPPVASDIGVSLGAAAAVAVELGDRIAPMGDTAAWGPEFSPDQVRAALDRTGLAYREPANLEREVAALIASGKVVGWAQGRGEVGPRALGQRSLLGSAHSPTMRDHINLRVKDREWWRPFAPSMLRSVSDQVLEVDADFPYMIMTTKVRAAYAERLPSVVHEDWSTRPQTVTEASNPRYHRMLTELGDLVGDPVCLNTSFNDRGEPIVSSPADALLTFSRLPIDALAVGPYLVTK 566
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeeee..eeeeeeehhhhhh........hhhhhhhhhhhh..hhhhh.eeee..hhhhhhhhhh.....hhhhhhhhhh............eee.hhhhhhhhhhhh......eeeeee......eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhh.....hhhhhhhhhh...........eeee..eeee..............hhhhhhhhhhhhhhhhh......eeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhh........hhhhhhhhhhhh...eeee.............eeeeee....hhhhhhhhhh..........eeee..hhhhhh............ee.hhhhhh.hhhhh....ee..eee....hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhh...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ver A   1 MRVLGLNGWPRDFHDASAALLVDGRIAAFAEEERFTRKKHGYNTAPVQAAAFCLAQAGLTVDDLDAVAFGWDLPAMYRERLGGWPHSDSEALDILLPRDVFPRRTDPPLHFVQHHLAHAASAYYFSGEDRGAVLIVDGQGEEECVTLAHAEGGKITVLDTVPGAWSLGFFYEHVSEYTGLGGDNPGKLMGLAAHGTTVDETLSAFAFDSDGYRLNLIDPQARDPEDWDEYSVTERAWFAHLERIYRLPPNEFVRRYDPAKGRVVRDTRRDPYEYRDLAATAQAALERAVFGLADSVLARTGERTLFVAGGVGLNATMNGKLLTRSTVDKMFVPPVASDIGVSLGAAAAVAVELGDRIAPMGDTAAWGPEFSPDQVRAALDRTGLAYREPANLEREVAALIASGKVVGWAQGRGEVGPRALGQRSLLGSAHSPTMRDHINLRVKDREWWRPFAPSMLRSVSDQVLEVDADFPYMIMTTKVRAAYAERLPSVVHEDWSTRPQTVTEASNPRYHRMLTELGDLVGDPVCLNTSFNDRGEPIVSSPADALLTFSRLPIDALAVGPYLVTK 566
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560

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 3VER)

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

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

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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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ver)

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	3ver
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		Orientation in Membranes	:	OPM
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	TOBZ_STRSD \| Q70IY1
		Comparative Protein Structure Models	:	ModBase
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	2.1.3.-
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		Disease Information	:	OMIM

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

3ven	TOBZ
3veo	TOBZ IN COMPLEX WITH CARBAMOYL PHOSPHATE
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

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Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (12, 12)

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