4BAJ - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   MYCOBACTERIUM TUBERCULOSIS CHORISMATE SYNTHASE AFTER EXPOSURE TO 266NM UV LASER

Authors :   P. J. B. Pereira, A. Royant, S. Panjikar, D. De Sanctis

Date :   14 Sep 12 (Deposition) - 17 Apr 13 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. B. Pereira, A. Royant, S. Panjikar, D. De Sanctis
In-House Uv Radiation-Damage-Induced Phasing Of Selenomethionine-Labeled Protein Structures.
J. Struct. Biol. V. 181 89 2013
PubMed-ID: 23178456 | Reference-DOI: 10.1016/J.JSB.2012.11.003

Molecule 1 - CHORISMATE SYNTHASE
	Chains	:	A
	EC Number	:	4.2.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE PHOSPHOLYASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 44)

No.	Name	Count	Type	Full Name
1	ACT	8	Ligand/Ion	ACETATE ION
2	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:4 , ASP A:241 , MSE A:357 , HOH A:2005 , HOH A:2055 , HOH A:2110 , HOH A:2122	BINDING SITE FOR RESIDUE ACT A1393
2	AC2	SOFTWARE	ALA A:172 , GLN A:208 , LEU A:219 , ARG A:271 , ARG A:273 , HOH A:2073	BINDING SITE FOR RESIDUE ACT A1394

(no "SS Bond" information available for 4BAJ)

(no "Cis Peptide Bond" information available for 4BAJ)

(no "SAP(SNP)/Variant" information available for 4BAJ)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_SYNTHASE_1	PS00787	Chorismate synthase signature 1.	AROC_MYCTO	8-23	1	A:8-23
1	CHORISMATE_SYNTHASE_1	PS00787	Chorismate synthase signature 1.	AROC_MYCTU	8-23	1	A:8-23
2	CHORISMATE_SYNTHASE_2	PS00788	Chorismate synthase signature 2.	AROC_MYCTO	134-150	1	A:134-150
2	CHORISMATE_SYNTHASE_2	PS00788	Chorismate synthase signature 2.	AROC_MYCTU	134-150	1	A:134-150
3	CHORISMATE_SYNTHASE_3	PS00789	Chorismate synthase signature 3.	AROC_MYCTO	341-357	1	A:346-357
3	CHORISMATE_SYNTHASE_3	PS00789	Chorismate synthase signature 3.	AROC_MYCTU	341-357	1	A:346-357

Biological Unit 1 (3, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_SYNTHASE_1	PS00787	Chorismate synthase signature 1.	AROC_MYCTO	8-23	4	A:8-23
1	CHORISMATE_SYNTHASE_1	PS00787	Chorismate synthase signature 1.	AROC_MYCTU	8-23	4	A:8-23
2	CHORISMATE_SYNTHASE_2	PS00788	Chorismate synthase signature 2.	AROC_MYCTO	134-150	4	A:134-150
2	CHORISMATE_SYNTHASE_2	PS00788	Chorismate synthase signature 2.	AROC_MYCTU	134-150	4	A:134-150
3	CHORISMATE_SYNTHASE_3	PS00789	Chorismate synthase signature 3.	AROC_MYCTO	341-357	4	A:346-357
3	CHORISMATE_SYNTHASE_3	PS00789	Chorismate synthase signature 3.	AROC_MYCTU	341-357	4	A:346-357

(no "Exon" information available for 4BAJ)

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:375
 aligned with AROC_MYCTO | P9WPY0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           AROC_MYCTO     2 LRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVLSGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAGMLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPPPRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSGDHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLEGGMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVALVLARAALEKFGGDSLAETQRNIAAYQRSVADR 392
               SCOP domains d4baja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeee........hhhhhhhhhhhhh...-----------.eeeee.ee..ee....eeeeee..hhhhhh........hhhhhhhhhhhh.........hhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee.hhhhhh..hhhhhh..ee......ee.......ee..ee....eeeeeee..........eee......eee....-----hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4baj A   2 LRWITAGESHGRALVAVVEGmVAGVHVTSADIADQLARRRLGY-----------AVTVLSGIRHGSTLGGPIAIEIGNTEWPKWETVmAADPVDPAELADVARNAPLTRPRPGHADYAGmLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPPPRAEDLPAIDASPVRAYDKAAEADmIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSGDHRLDSQLAAAVmGIQAIKGVEIGDGFQTARRRGSRAHDEmYPGPDGVVRSTNRAGGLEGGmTNGQPLRVRAAmKPISTVPRALATVDLATGDEAVAIHQ-----AVPAAGVVVETmVALVLARAALEKFGGDSLAETQRNIAAYQRSVADR 392
                                    11        21|       31        41  |      -    |   61        71        81       |91       101       111       121       131       141       151       161       171       181       191       201   |   211       221       231       241       251 |     261       271       281       291       301|      311  |    321       331        |-    |  351     | 361       371       381       391 
                                               22-MSE                44          56                               89-MSE                         121-MSE                                                                             205-MSE                                         253-MSE                     281-MSE              302-MSE     314-MSE                   340   346        357-MSE

Chain A from PDB  Type:PROTEIN  Length:375
 aligned with AROC_MYCTU | P9WPY1 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           AROC_MYCTU     2 LRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVLSGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAGMLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPPPRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSGDHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLEGGMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVALVLARAALEKFGGDSLAETQRNIAAYQRSVADR 392
               SCOP domains d4baja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeee........hhhhhhhhhhhhh...-----------.eeeee.ee..ee....eeeeee..hhhhhh........hhhhhhhhhhhh.........hhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee.hhhhhh..hhhhhh..ee......ee.......ee..ee....eeeeeee..........eee......eee....-----hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------CHORISMATE_SYNTH--------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHORISMATE_SYNTHA----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4baj A   2 LRWITAGESHGRALVAVVEGmVAGVHVTSADIADQLARRRLGY-----------AVTVLSGIRHGSTLGGPIAIEIGNTEWPKWETVmAADPVDPAELADVARNAPLTRPRPGHADYAGmLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPPPRAEDLPAIDASPVRAYDKAAEADmIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSGDHRLDSQLAAAVmGIQAIKGVEIGDGFQTARRRGSRAHDEmYPGPDGVVRSTNRAGGLEGGmTNGQPLRVRAAmKPISTVPRALATVDLATGDEAVAIHQ-----AVPAAGVVVETmVALVLARAALEKFGGDSLAETQRNIAAYQRSVADR 392
                                    11        21|       31        41  |      -    |   61        71        81       |91       101       111       121       131       141       151       161       171       181       191       201   |   211       221       231       241       251 |     261       271       281       291       301|      311  |    321       331        |-    |  351     | 361       371       381       391 
                                               22-MSE                44          56                               89-MSE                         121-MSE                                                                             205-MSE                                         253-MSE                     281-MSE              302-MSE     314-MSE                   340   346        357-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Chorismate synthase, AroC (18)

Superfamily: Chorismate synthase, AroC (18)

Family: Chorismate synthase, AroC (14)

Protein domain: automated matches (3)

Mycobacterium tuberculosis [TaxId: 1773] (2)

d4baja_

(no "CATH Domain" information available for 4BAJ)

(no "Pfam Domain" information available for 4BAJ)

Asymmetric Unit(hide GO term definitions)

Chain A (AROC_MYCTU | P9WPY1)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0004107	chorismate synthase activity	Catalysis of the reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.
	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:0016651	oxidoreductase activity, acting on NAD(P)H	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	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:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A (AROC_MYCTO | P9WPY0)

molecular function
	GO:0004107	chorismate synthase activity	Catalysis of the reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.
	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.
biological process
	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:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Asymmetric Unit
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Biological Unit
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	4baj
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	4.2.3.5
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UniProtKB/Swiss-Prot
	AROC_MYCTO \| P9WPY0	:	1ztb 2g85 2o11 2o12 2qhf 4bai
	AROC_MYCTU \| P9WPY1	:	1ztb 2g85 2o11 2o12 2qhf 4bai

1ztb	CRYSTAL STRUCTURE OF CHORISMATE SYNTHASE FROM MYCOBACTERIUMTUBERCULOSIS
4bai	MYCOBACTERIUM TUBERCULOSIS CHORISMATE SYNTHASE BEFORE EXPOSURE TO 266 NM UV LASER

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (11, 16)

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