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Title :   X-RAY CRYSTAL STRUCTURE OF A TYROSINE AMINOMUTASE MUTANT CONSTRUCT WITH BOUND LIGAND

Authors :   H. A. Cooke, S. D. Bruner

Date :   23 Oct 09 (Deposition) - 07 Jul 10 (Release) - 07 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Mio, Aminomutase, Enediyne, Transferase, Histidine Metabolism, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. A. Cooke, S. D. Bruner
Probing The Active Site Of Mio-Dependent Aminomutases, Key Catalysts In The Biosynthesis Of Beta-Amino Acids Incorporated In Secondary Metabolites
Biopolymers V. 93 802 2010
PubMed-ID: 20577998 | Reference-DOI: 10.1002/BIP.21500

Molecule 1 - HISTIDINE AMMONIA-LYASE
	Chains	:	A, B
	EC Number	:	4.3.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SGCC4
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES GLOBISPORUS
	Organism Taxid	:	1908

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MDO	2	Mod. Amino Acid	{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2	TYR	2	Mod. Amino Acid	TYROSINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MDO	2	Mod. Amino Acid	{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2	TYR	2	Mod. Amino Acid	TYROSINE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	MDO	4	Mod. Amino Acid	{2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL-1-YL}ACETIC ACID
2	TYR	4	Mod. Amino Acid	TYROSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:63 , TYR A:69 , HIS A:93 , MDO A:152 , ASN A:205 , ASN A:341 , PHE A:356 , TYR A:415 , ASN A:438 , GLN A:442 , HOH A:673 , TYR B:308 , ARG B:311	BINDING SITE FOR RESIDUE TYR A 600
2	AC2	SOFTWARE	GLN A:305 , TYR A:308 , ARG A:311 , PHE B:63 , TYR B:69 , HIS B:93 , MDO B:152 , LEU B:156 , ASN B:205 , ASN B:341 , PHE B:356 , TYR B:415 , GLN B:442 , HOH B:690 , HOH B:692	BINDING SITE FOR RESIDUE TYR B 600

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

Asymmetric Unit

No.	Residues
1	Asn A:341	-	Pro A:342
2	Asn B:341	-	Pro B:342

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAL_HISTIDASE	PS00488	Phenylalanine and histidine ammonia-lyases signature.	TAM_STRGL	148-164	2	A:148-164 B:148-164

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAL_HISTIDASE	PS00488	Phenylalanine and histidine ammonia-lyases signature.	TAM_STRGL	148-164	2	A:148-164 B:148-164

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAL_HISTIDASE	PS00488	Phenylalanine and histidine ammonia-lyases signature.	TAM_STRGL	148-164	4	A:148-164 B:148-164

(no "Exon" information available for 3KDZ)

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:528
 aligned with TAM_STRGL | Q8GMG0 from UniProtKB/Swiss-Prot  Length:539

    Alignment length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          539 
                                    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        |-
            TAM_STRGL    11 VPVSVDGETLTVEAVRRVAEERATVDVPAESIAKAQKSREIFEGIAEQNIPIYGVTTGYGEMIYMQVDKSKEVELQTNLVRSHSAGVGPLFAEDEARAIVAARLNTLAKGHSAVRPIILERLAQYLNEGITPAIPEIGSLGASGDLAPLSHVASTLIGEGYVLRDGRPVETAQVLAERGIEPLELRFKEGLALINGTSGMTGLGSLVVGRALEQAQQAEIVTALLIEAVRGSTSPFLAEGHDIARPHEGQIDTAANMRALMRGSGLTVEHADLRRELQKDKEAGKDVQRSEIYLQKAYSLRAIPQVVGAVRDTLYHARHKLRIELNSANDNPLFFEGKEIFHGANFHGQPIAFAMDFVTIALTQLGVLAERQINRVLNRHLSYGLPEFLVSGDPGLHSGFAGAQYPATALVAENRTIGPASTQSVPSNGDNQDVVSMGLISARNARRVLSNNNKILAVEYLAAAQAVDISGRFDGLSPAAKATYEAVRRLVPTLGVDRYMADDIELVADALSRGEFLRAIARETDIQLR-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......hhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh...........hhhhh.eee...hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eee.....--hhhhhhhhhhhhh...eeee..eeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhh......ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh............hhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdz A  11 VPVSVDGETLTVEAVRRVAEERATVDVPAESIAKAQKSREIFEGIAEQNIPIFGVTTGYGEMIYMQVDKSKEVELQTNLVRSHSAGVGPLFAEDEARAIVAARLNTLAKGHSAVRPIILERLAQYLNEGITPAIPEIGSLGa--DLAPLSHVASTLIGEGYVLRDGRPVETAQVLAERGIEPLELRFKEGLALINGTSGMTGLGSLVVGRALEQAQQAEIVTALLIEAVRGSTSPFLAEGHDIARPHEGQIDTAANMRALMRGSGLTVEHADLRRELQKDKEAGKDVQRSEIYLQKAYSLRAIPQVVGAVRDTLYHARHKLRIELNSANDNPLFFEGKEIFHGANFHGQPIAFAMDFVTIALTQLGVLAERQINRVLNRHLSYGLPEFLVSGDPGLHSGFAGAQYPATALVAENRTIGPASTQSVPSNGDNQDVVSMGLISARNARRVLSNNNKILAVEYLAAAQAVDISGRFDGLSPAAKATYEAVRRLVPTLGVDRYMADDIELVADALSRGEFLRAIARETDIQLRY 600
                                    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       600
                                                                                                                                                                       152-MDO                                                                                                                                                                                                                                                                                                                                                                                            539|
                                                                                                                                                                          155                                                                                                                                                                                                                                                                                                                                                                                              600

Chain B from PDB  Type:PROTEIN  Length:528
 aligned with TAM_STRGL | Q8GMG0 from UniProtKB/Swiss-Prot  Length:539

    Alignment length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          539 
                                    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        |-
            TAM_STRGL    11 VPVSVDGETLTVEAVRRVAEERATVDVPAESIAKAQKSREIFEGIAEQNIPIYGVTTGYGEMIYMQVDKSKEVELQTNLVRSHSAGVGPLFAEDEARAIVAARLNTLAKGHSAVRPIILERLAQYLNEGITPAIPEIGSLGASGDLAPLSHVASTLIGEGYVLRDGRPVETAQVLAERGIEPLELRFKEGLALINGTSGMTGLGSLVVGRALEQAQQAEIVTALLIEAVRGSTSPFLAEGHDIARPHEGQIDTAANMRALMRGSGLTVEHADLRRELQKDKEAGKDVQRSEIYLQKAYSLRAIPQVVGAVRDTLYHARHKLRIELNSANDNPLFFEGKEIFHGANFHGQPIAFAMDFVTIALTQLGVLAERQINRVLNRHLSYGLPEFLVSGDPGLHSGFAGAQYPATALVAENRTIGPASTQSVPSNGDNQDVVSMGLISARNARRVLSNNNKILAVEYLAAAQAVDISGRFDGLSPAAKATYEAVRRLVPTLGVDRYMADDIELVADALSRGEFLRAIARETDIQLR-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......hhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh...........hhhhhhhee...hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.ee..eee.....--hhhhhhhhhhhhh...eeee..eeeehhhhhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.........hhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------PAL_HISTIDASE    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdz B  11 VPVSVDGETLTVEAVRRVAEERATVDVPAESIAKAQKSREIFEGIAEQNIPIFGVTTGYGEMIYMQVDKSKEVELQTNLVRSHSAGVGPLFAEDEARAIVAARLNTLAKGHSAVRPIILERLAQYLNEGITPAIPEIGSLGa--DLAPLSHVASTLIGEGYVLRDGRPVETAQVLAERGIEPLELRFKEGLALINGTSGMTGLGSLVVGRALEQAQQAEIVTALLIEAVRGSTSPFLAEGHDIARPHEGQIDTAANMRALMRGSGLTVEHADLRRELQKDKEAGKDVQRSEIYLQKAYSLRAIPQVVGAVRDTLYHARHKLRIELNSANDNPLFFEGKEIFHGANFHGQPIAFAMDFVTIALTQLGVLAERQINRVLNRHLSYGLPEFLVSGDPGLHSGFAGAQYPATALVAENRTIGPASTQSVPSNGDNQDVVSMGLISARNARRVLSNNNKILAVEYLAAAQAVDISGRFDGLSPAAKATYEAVRRLVPTLGVDRYMADDIELVADALSRGEFLRAIARETDIQLRY 600
                                    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       600
                                                                                                                                                                       152-MDO                                                                                                                                                                                                                                                                                                                                                                                            539|
                                                                                                                                                                          155                                                                                                                                                                                                                                                                                                                                                                                              600

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 3KDZ)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (TAM_STRGL | Q8GMG0)

molecular function
	GO:0016841	ammonia-lyase activity	Catalysis of the release of ammonia by the cleavage of a carbon-nitrogen bond or the reverse reaction with ammonia as a substrate.
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0050368	tyrosine 2,3-aminomutase activity	Catalysis of the reaction: L-tyrosine = 3-amino-3-(4-hydroxyphenyl)propanoate.
	GO:0052883	tyrosine ammonia-lyase activity	Catalysis of the reaction: L-tyrosine = NH(4)(+) + trans-4-coumarate.
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:0009403	toxin biosynthetic process	The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:341 - Pro A:342	[ RasMol ]
		Asn B:341 - Pro B:342	[ RasMol ]

Biological Units
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	3kdz
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	4.3.1.3
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UniProtKB/Swiss-Prot
	TAM_STRGL \| Q8GMG0	:	2ohy 2qve 2rjr 2rjs 3kdy

2ohy	X-RAY CRYSTAL STRUCTURE OF TYROSINE AMINOMUTASE FROM STREPTOMYCES GLOBISPORUS
2qve	CRYSTAL STRUCTURE OF SGTAM BOUND TO MECHANISM BASED INHIBITOR
2rjr	SUBSTRATE MIMIC BOUND TO SGTAM
2rjs	SGTAM BOUND TO SUBSTRATE MIMIC
3kdy	X-RAY CRYSTAL STRUCTURE OF TYROSINE AMINOMUTASE MUTANT CONSTRUCT

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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