3CSM - JenaLib

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Title :   STRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOXABICYCLIC INHIBITOR

Authors :   N. Straeter, G. Schnappauf, G. Braus, W. N. Lipscomb

Date :   10 Jul 97 (Deposition) - 14 Jan 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B  (2x)

Keywords :   Chorismate Pyruvatemutase, Allosteric Protein, Complex (Isomerase- Peptide), Transition State Analog, Complex (Isomerase-Peptide) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Strater, G. Schnappauf, G. Braus, W. N. Lipscomb
Mechanisms Of Catalysis And Allosteric Regulation Of Yeast Chorismate Mutase From Crystal Structures.
Structure V. 5 1437 1997
PubMed-ID: 9384560 | Reference-DOI: 10.1016/S0969-2126(97)00294-3
(for further references see the PDB file header)

Molecule 1 - CHORISMATE MUTASE
	Chains	:	A, B
	EC Number	:	5.4.99.5
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PME605
	Expression System Strain	:	RH1242
	Expression System Taxid	:	4932
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	RH1242
	Synonym	:	CHORISMATE PYRUVATE MUTASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	TRP	2	Mod. Amino Acid	TRYPTOPHAN
2	TSA	2	Ligand/Ion	8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	TRP	2	Mod. Amino Acid	TRYPTOPHAN
2	TSA	2	Ligand/Ion	8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	TRP	2	Mod. Amino Acid	TRYPTOPHAN
2	TSA	2	Ligand/Ion	8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	TRP	2	Mod. Amino Acid	TRYPTOPHAN
2	TSA	2	Ligand/Ion	8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:71 , ILE A:74 , ARG A:76 , SER A:79 , ILE A:98 , TYR A:100 , ASN A:138 , ASN A:139 , PHE A:140 , GLY A:141 , SER A:142	BINDING SITE FOR RESIDUE TRP A 300
2	AC2	SOFTWARE	HIS B:71 , ILE B:74 , ARG B:76 , SER B:79 , ILE B:98 , TYR B:100 , ASN B:138 , ASN B:139 , PHE B:140 , GLY B:141 , SER B:142	BINDING SITE FOR RESIDUE TRP B 300
3	AC3	SOFTWARE	ARG A:16 , ARG A:157 , LYS A:168 , ILE A:192 , THR A:193 , ASN A:194 , GLU A:198 , ILE A:201 , ILE A:239 , THR A:242 , LYS A:243 , GLU A:246	BINDING SITE FOR RESIDUE TSA A 400
4	AC4	SOFTWARE	ARG B:16 , ARG B:157 , LYS B:168 , ILE B:192 , THR B:193 , ASN B:194 , GLU B:198 , ILE B:201 , ILE B:239 , THR B:242 , LYS B:243 , GLU B:246	BINDING SITE FOR RESIDUE TSA B 400
5	ACB	UNKNOWN	ARG B:16 , LEU B:19 , LEU B:12 , VAL B:164 , ARG B:157 , THR B:242 , GLU B:246 , LYS B:243 , ILE B:239 , ASN B:194 , GLU B:198 , LYS B:168 , VAL B:197	ACTIVE SITE.
6	ACT	UNKNOWN	ARG A:16 , LEU A:19 , LEU A:12 , VAL A:164 , ARG A:157 , THR A:242 , GLU A:246 , LYS A:243 , ILE A:239 , ASN A:194 , GLU A:198 , LYS A:168 , VAL A:197	ACTIVE SITE.
7	REB	UNKNOWN	ILE B:74 , ARG B:75 , ARG B:76 , THR B:145 , GLY B:141 , SER B:142 , ASN B:139	REGULATORY BINDING SITE FOR TRYPTOPHAN AND TYROSINE.
8	REG	UNKNOWN	ILE A:74 , ARG A:75 , ARG A:76 , THR A:145 , GLY A:141 , SER A:142 , ASN A:139	REGULATORY BINDING SITE FOR TRYPTOPHAN AND TYROSINE.

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_3	PS51169	Chorismate mutase domain profile.	CHMU_YEAST	3-255	2	A:3-255 B:3-255

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_3	PS51169	Chorismate mutase domain profile.	CHMU_YEAST	3-255	2	A:3-255 B:3-255

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_3	PS51169	Chorismate mutase domain profile.	CHMU_YEAST	3-255	2	A:3-255 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_3	PS51169	Chorismate mutase domain profile.	CHMU_YEAST	3-255	2	- B:3-255

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPR060C	1	YPR060C.1	XVI:675628-674858	771	CHMU_YEAST	1-256	256	2	A:1-256 (gaps) B:1-256 (gaps)	256 256

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:253
 aligned with CHMU_YEAST | P32178 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:257
                                                                                                                                                                                                                                                                                         256 
                                    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     | 
           CHMU_YEAST     1 MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLISKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKNITNSAVEEKILERLTKKAEVYGVDPTNESGERRITPEYLVKIYKEIVIPITKEVEVEYLLRRLEE-   -
               SCOP domains d3csma_ A: Allosteric chorismate mutase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3csmA00 A:1-256 Chorismate Mutase, subunit A                                                                                                                                                                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhh....hhh........hhhhhhhhhhhhhhhh.hhh........hhh..................hhh...hhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhh.....----.....hhhhhhhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_3  PDB: A:3-255 UniProt: 3-255                                                                                                                                                                                                                -- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-256 (gaps) UniProt: 1-256                                                                                                                                                                                                                    - Transcript 1
                 3csm A   1 MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLISKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKNITNSAVEEKILERLTKKAEVYGVDPT----ERRITPEYLVKIYKEIVIPITKEVEVEYLLRRLEEW 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      |  - |     230       240       250     ||
                                                                                                                                                                                                                                                  217  222                               256|
                                                                                                                                                                                                                                                                                          300

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with CHMU_YEAST | P32178 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:257
                                                                                                                                                                                                                                                                                         256 
                                    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     | 
           CHMU_YEAST     1 MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLISKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKNITNSAVEEKILERLTKKAEVYGVDPTNESGERRITPEYLVKIYKEIVIPITKEVEVEYLLRRLEE-   -
               SCOP domains d3csmb_ B: Allosteric chorismate mutase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3csmB00 B:1-256 Chorismate Mutase, subunit A                                                                                                                                                                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhh....hhh........hhhhhhhhhhhhhhhh.hhh........hhh..................hhh...hhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhh.....----.....hhhhhhhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_3  PDB: B:3-255 UniProt: 3-255                                                                                                                                                                                                                -- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-256 (gaps) UniProt: 1-256                                                                                                                                                                                                                    - Transcript 1
                 3csm B   1 MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLISKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIMKNITNSAVEEKILERLTKKAEVYGVDPT----ERRITPEYLVKIYKEIVIPITKEVEVEYLLRRLEEW 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      |  - |     230       240       250     ||
                                                                                                                                                                                                                                                  217  222                               256|
                                                                                                                                                                                                                                                                                          300

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Chorismate mutase II (21)

Superfamily: Chorismate mutase II (21)

Family: Allosteric chorismate mutase (5)

Protein domain: Allosteric chorismate mutase (5)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (5)

1a	d3csma_	A:
1b	d3csmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Chorismate Mutase, subunit A (5)

Homologous Superfamily: Chorismate Mutase, subunit A (5)

Baker's yeast (Saccharomyces cerevisiae) (5)

1a	3csmA00	A:1-256
1b	3csmB00	B:1-256

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHMU_YEAST | P32178)

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:0004106	chorismate mutase activity	Catalysis of the reaction: chorismate = prephenate.
	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.
biological process
	GO:0009094	L-phenylalanine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0046417	chorismate metabolic process	The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.
	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:0006571	tyrosine biosynthetic process	The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

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