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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF THE TYCC5-6 PCP-C BIDOMAIN OF THE TYROCIDINE SYNTHETASE TYCC

Authors :   S. A. Samel, G. Schoenafinger, T. A. Knappe, M. A. Marahiel, L. -O. Essen

Date :   13 Feb 07 (Deposition) - 30 Oct 07 (Release) - 13 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Multifunctional Enzyme, Antibiotic Biosynthesis, Condensation Domain, Peptide Bond Formation, Ligase, Tyrocidine, Antibiotics, Phosphopantetheine, Nonribosomal Peptide Synthetase, Peptidyl Carrier Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Samel, G. Schoenafinger, T. A. Knappe, M. A. Marahiel, L. -O. Esse
Structural And Functional Insights Into A Peptide Bond- Forming Bidomain From A Nonribosomal Peptide Synthetase.
Structure V. 15 781 2007
PubMed-ID: 17637339 | Reference-DOI: 10.1016/J.STR.2007.05.008

Molecule 1 - TYROCIDINE SYNTHETASE 3
	Atcc	:	8185
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Variant	:	PREP4
	Expression System Vector	:	PQE61
	Fragment	:	PCP-C BIDOMAIN OF TYCC MODULE 5 AND 6, RESIDUES 5116-5633
	Organism Scientific	:	BREVIBACILLUS BREVIS
	Organism Taxid	:	1393
	Synonym	:	TYROCIDINE SYNTHETASE III, NON-RIBOSOMAL PEPTIDE SYNTHETASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	DIO	2	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	NA	1	Ligand/Ion	SODIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:224 , ASP A:228 , GLY A:229 , HOH A:2290	BINDING SITE FOR RESIDUE SO4 A1523
2	AC2	SOFTWARE	GLY A:40 , HIS A:42 , LEU A:44 , ARG A:45 , HOH A:2291 , HOH A:2293	BINDING SITE FOR RESIDUE SO4 A1524
3	AC3	SOFTWARE	PHE A:142 , LEU A:235	BINDING SITE FOR RESIDUE DIO A1525
4	AC4	SOFTWARE	GLN A:29 , VAL A:158 , GLN A:325 , ALA A:326 , GLY A:328	BINDING SITE FOR RESIDUE DIO A1526
5	AC5	SOFTWARE	GLN A:398 , ASP A:402 , HOH A:2021 , HOH A:2250	BINDING SITE FOR RESIDUE NA A1527

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:201	-	Pro A:202

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARRIER	PS50075	Carrier protein (CP) domain profile.	TYCC_BREPA	965-1040 2002-2077 3040-3115 4075-4150 5119-5194 6162-6237	1	- - - - A:8-83 -
2	PHOSPHOPANTETHEINE	PS00012	Phosphopantetheine attachment site.	TYCC_BREPA	995-1010 2032-2047 3070-3085 4105-4120 5149-5164 6192-6207	1	- - - - A:38-53 -

(no "Exon" information available for 2JGP)

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:520
 aligned with TYCC_BREPA | O30409 from UniProtKB/Swiss-Prot  Length:6486

    Alignment length:520
                                  5123      5133      5143      5153      5163      5173      5183      5193      5203      5213      5223      5233      5243      5253      5263      5273      5283      5293      5303      5313      5323      5333      5343      5353      5363      5373      5383      5393      5403      5413      5423      5433      5443      5453      5463      5473      5483      5493      5503      5513      5523      5533      5543      5553      5563      5573      5583      5593      5603      5613      5623      5633
          TYCC_BREPA   5114 TTEYVAPRSVWEARLAQVWEQVLNVPQVGALDDFFALGGHSLRAMRVLSSMHNEYQVDIPLRILFEKPTIQELAAFIEETAKGNVFSIEPVQKQAYYPVSSAQKRMYILDQFEGVGISYNMPSTMLIEGKLERTRVEAAFQRLIARHESLRTSFAVVNGEPVQNIHEDVPFALAYSEVTEQEARELVSSLVQPFDLEVAPLIRVSLLKIGEDRYVLFTDMHHSISDGVSSGILLAEWVQLYQGDVLPELRIQYKDFAVWQQEFSQSAAFHKQEAYWLQTFADDIPVLNLPTDFTRPSTQSFAGDQCTIGAGKALTEGLHQLAQATGTTLYMVLLAAYNVLLAKYAGQEDIIVGTPITGRSHADLEPIVGMFVNTLAMRNKPQREKTFSEFLQEVKQNALDAYGHQDYPFEELVEKLAIARDLSRNPLFDTVFTFQNSTEEVMTLPECTLAPFMTDETGQHAKFDLTFSATEEREEMTIGVEYSTSLFTRETMERFSRHFLTIAASIVQNPHIRLGEIDML 5633
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------PP-binding-2jgpA02 A:15-79                                       ---------------Condensation-2jgpA01 A:95-384                                                                                                                                                                                                                                                                     --------------------HxxPF_rpt-2jgpA03 A:405-497                                                                  ------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhh................ee.hhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee........eeee.hhhhhhhhhhhh...........eeeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhh......................eeeeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhh.......eeeeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.............eeeeee...........eeeee.............eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CARRIER  PDB: A:8-83 UniProt: 5119-5194                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------PHOSPHOPANTETHEI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2jgp A    3 RSEYVAPRSVWEARLAQVWEQVLNVPQVGALDDFFALGGHSLRAMRVLSSMHNEYQVDIPLRILFEKPTIQELAAFIEETAKGNVFSIEPVQKQAYYPVSSAQKRMYILDQFEGVGISYNMPSTMLIEGKLERTRVEAAFQRLIARHESLRTSFAVVNGEPVQNIHEDVPFALAYSEVTEEEARELVSSLVQPFDLEVAPLIRVSLLKIGEDRYVLFTDMHHSISDGVSSGILLAEWVQLYQGDVLPELRIQYKDFAVWQQEFSQSAAFHKQEAYWLQTFADDIPVLNLPTDFTRPSTQSFAGDQCTIGAGKALTEGLHQLAQATGTTLYMVLLAAYNVLLAKYAGQEDIIVGTPITGRSHADLEPIVGMFVNTLAMRNKPQREKTFSEFLQEVKQNALDAYGHQDYPFEELVEKLAIARDLSRNPLFDTVFTFQNSTEEVMTLPECTLAPFMTDETGQHAKFDLTFSATEEREEMTIGVEYSTSLFTRETMERFSRHFLTIAASIVQNPHIRLGEIDML  522
                                    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       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522

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 2JGP)

(no "CATH Domain" information available for 2JGP)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CoA-acyltrans (22)

Family: Condensation (3)

Brevibacillus parabrevis (1)

Condensation-2jgpA01

A:95-384

Clan: PP-binding (27)

Family: PP-binding (27)

Brevibacillus parabrevis (2)

PP-binding-2jgpA02

A:15-79

Clan: no clan defined [family: HxxPF_rpt] (1)

Family: HxxPF_rpt (1)

Brevibacillus parabrevis (1)

HxxPF_rpt-2jgpA03

A:405-497

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TYCC_BREPA | O30409)

molecular function
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	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:0031177	phosphopantetheine binding	Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:201 - Pro A:202	[ RasMol ]

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	2jgp
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	TYCC_BREPA \| O30409	:	1dny 2gdw 2gdx 2gdy 2ge1 2k2q 2md9 4mrt

1dny	SOLUTION STRUCTURE OF PCP, A PROTOTYPE FOR THE PEPTIDYL CARRIER DOMAINS OF MODULAR PEPTIDE SYNTHETASES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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