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Biol. Unit 1 - sites

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Description

Title :   TETRACENOMYCIN ARO/CYC NAI STRUCTURE

Authors :   B. D. Ames, S. C. Tsai

Date :   27 Sep 07 (Deposition) - 22 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (1x)

Keywords :   Tetracenomycin, Polyketide, Aromatase, Cyclase, Dehydratase, Helix-Grip, Double-Hot-Dog, Antibiotic Biosynthesis, Methyltransferase, Multifunctional Enzyme, Transferase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Ames, T. P. Korman, W. Zhang, P. Smith, T. Vu, Y. Tang, S. C. Tsai
Crystal Structure And Functional Analysis Of Tetracenomycin Aro/Cyc: Implications For Cyclization Specificity Of Aromatic Polyketides.
Proc. Natl. Acad. Sci. Usa V. 105 5349 2008
PubMed-ID: 18388203 | Reference-DOI: 10.1073/PNAS.0709223105
(for further references see the PDB file header)

Compounds

Molecule 1 - MULTIFUNCTIONAL CYCLASE-DEHYDRATASE-3-O-METHYL TRANSFERASE TCMN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	TCMN
	Organism Scientific	:	STREPTOMYCES GLAUCESCENS
	Organism Taxid	:	1907

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 7)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	IOD	5	Ligand/Ion	IODIDE ION

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	IOD	10	Ligand/Ion	IODIDE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	IOD	5	Ligand/Ion	IODIDE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:82 , GLU A:84 , GLY A:86 , PRO A:87 , PHE A:88 , HOH A:287	BINDING SITE FOR RESIDUE ACT A 155
2	AC2	SOFTWARE	GLU A:34 , TRP A:63 , TRP A:65 , ARG A:82 , HOH A:286	BINDING SITE FOR RESIDUE ACT A 156
3	AC3	SOFTWARE	ARG A:82	BINDING SITE FOR RESIDUE IOD A 157
4	AC4	SOFTWARE	ARG A:149 , GLY A:151	BINDING SITE FOR RESIDUE IOD A 159
5	AC5	SOFTWARE	ARG A:147 , HOH A:162 , HOH A:260	BINDING SITE FOR RESIDUE IOD A 161

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2REZ)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2REZ)

Exons (0, 0)

(no "Exon" information available for 2REZ)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:155
 aligned with TCMN_STRGA | P16559 from UniProtKB/Swiss-Prot  Length:494

    Alignment length:155
                               1                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147     
           TCMN_STRGA     - ---MAARTDNSIVVNAPFELVWDVTNDIEAWPELFSEYAEAEILRQDGDGFDFRLKTRPDANGRVWEWVSHRVPDKGSRTVRAHRVETGPFAYMNLHWTYRAVAGGTEMRWVQEFDMKPGAPFDNAHMTAHLNTTTRANMERIKKIIEDRHREGQ 152
               SCOP domains d2reza_ A: Multifunctional enzyme TcmN, cyclase/aromatase domain                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Polyketide_cyc-2rezA01 A:11-141                                                                                                    ----------- Pfam domains
         Sec.struct. author .....eeeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee.........eeeeeeeeehhh.eeeeee.....eeeeeeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rez A  -2 GSHMAARTDNSIVVNAPFELVWDVTNDIEAWPELFSEYAEAEILRQDGDGFDFRLKTRPDANGRVWEWVSHRVPDKGSRTVRAHRVETGPFAYMNLHWTYRAVAGGTEMRWVQEFDMKPGAPFDNAHMTAHLNTTTRANMERIKKIIEDRHREGQ 152
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: TBP-like (289)

Superfamily: Bet v1-like (158)

Family: oligoketide cyclase/dehydrase-like (7)

Protein domain: Multifunctional enzyme TcmN, cyclase/aromatase domain (4)

Streptomyces glaucescens [TaxId: 1907] (4)

d2reza_

CATH Domains (0, 0)

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

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Bet_V_1_like (93)

Family: Polyketide_cyc (8)

Streptomyces glaucescens (2)

Polyketide_cyc-2rezA01

A:11-141

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (TCMN_STRGA | P16559)

molecular function
	GO:0008171	O-methyltransferase activity	Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
	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:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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: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: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.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	TCMN_STRGA \| P16559	:	2rer 2res 3tvq

Related Entries Specified in the PDB File

2rer	SAME PROTEIN WITHOUT BOUND IODIDE
2res	SAME PROTEIN WITH R69A MUTATION