2H9D - JenaLib

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Title :   PYRUVATE-BOUND STRUCTURE OF THE ISOCHORISMATE-PYRUVATE LYASE FROM PSEUDOMONAS AERUGIONSA

Authors :   A. L. Lamb, J. Zaitseva, J. Lu

Date :   09 Jun 06 (Deposition) - 15 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x)

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

Reference :   J. Zaitseva, J. Lu, K. L. Olechoski, A. L. Lamb
Two Crystal Structures Of The Isochorismate Pyruvate Lyase From Pseudomonas Aeruginosa.
J. Biol. Chem. V. 281 33441 2006
PubMed-ID: 16914555 | Reference-DOI: 10.1074/JBC.M605470200

Molecule 1 - SALICYLATE BIOSYNTHESIS PROTEIN PCHB
	Chains	:	A, B, C, D
	EC Number	:	4.1.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET29B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCHB
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PAO1
	Synonym	:	ISOCHORISMATE-PYRUVATE LYASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	PYR	6	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PYR	2	Ligand/Ion	PYRUVIC ACID

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PYR	4	Ligand/Ion	PYRUVIC ACID

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PYR	6	Ligand/Ion	PYRUVIC ACID

Biological Unit 4 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PYR	4	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:15 , ASP A:18 , HOH C:238 , GLU D:15 , ASP D:18 , HOH D:343	BINDING SITE FOR RESIDUE CA D 301
2	AC2	SOFTWARE	ARG C:14 , HOH C:211 , ALA D:38 , LYS D:42 , GLN D:90 , PYR D:202	BINDING SITE FOR RESIDUE PYR C 201
3	AC3	SOFTWARE	PYR C:201 , HOH C:211 , ARG D:31 , MET D:57 , TYR D:86 , ILE D:87 , GLN D:90	BINDING SITE FOR RESIDUE PYR D 202
4	AC4	SOFTWARE	ARG C:31 , ARG C:53 , MET C:57 , TYR C:86 , ILE C:87 , PYR C:206 , HOH C:249	BINDING SITE FOR RESIDUE PYR C 203
5	AC5	SOFTWARE	ARG B:31 , PRO B:49 , MET B:57 , ILE B:83 , GLN B:90	BINDING SITE FOR RESIDUE PYR B 204
6	AC6	SOFTWARE	ARG A:31 , VAL A:35 , MET A:57 , TYR A:86 , ILE A:87 , HOH A:214	BINDING SITE FOR RESIDUE PYR A 205
7	AC7	SOFTWARE	LYS C:42 , ARG C:53 , GLN C:90 , PYR C:203 , ARG D:14	BINDING SITE FOR RESIDUE PYR C 206

(no "SS Bond" information available for 2H9D)

(no "Cis Peptide Bond" information available for 2H9D)

(no "SAP(SNP)/Variant" information available for 2H9D)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_2	PS51168	Chorismate mutase domain profile.	PCHB_PSEAE	4-94	4	A:4-94 B:4-94 C:4-94 D:4-94

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_2	PS51168	Chorismate mutase domain profile.	PCHB_PSEAE	4-94	2	A:4-94 B:4-94 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_2	PS51168	Chorismate mutase domain profile.	PCHB_PSEAE	4-94	2	- - C:4-94 D:4-94

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_2	PS51168	Chorismate mutase domain profile.	PCHB_PSEAE	4-94	4	A:4-94 B:4-94 C:4-94 D:4-94

Biological Unit 4 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHORISMATE_MUT_2	PS51168	Chorismate mutase domain profile.	PCHB_PSEAE	4-94	4	A:4-94 B:4-94 C:4-94 D:4-94

(no "Exon" information available for 2H9D)

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:84
 aligned with PCHB_PSEAE | Q51507 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
           PCHB_PSEAE     1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYW  94
               SCOP domains d2h9da1 A:1-94 Salicylate biosynthesis pr          otein PchB                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CHORISMATE_MUT_2  PDB: A:4-94 UniProt: 4-94                                                 PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2h9d A   1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRF----------ERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYW  94
                                    10        20        30        40|        - |      60        70        80        90    
                                                                   41         52

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with PCHB_PSEAE | Q51507 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
           PCHB_PSEAE     2 KTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYW  94
               SCOP domains d2h9db_ B: Salicylate biosynthesis prote      in PchB                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CHORISMATE_MUT_2  PDB: B:4-94 UniProt: 4-94                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 2h9d B   2 KTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRF------IPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYW  94
                                    11        21        31        41      | 51        61        71        81        91   
                                                                  41     48

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with PCHB_PSEAE | Q51507 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
           PCHB_PSEAE     1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYWRQTR  98
               SCOP domains d2h9dc_ C: Salicylate biosynthesis protein PchB                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CHORISMATE_MUT_2  PDB: C:4-94 UniProt: 4-94                                                ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2h9d C   1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYWRQTR  98
                                    10        20        30        40        50        60        70        80        90

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with PCHB_PSEAE | Q51507 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           PCHB_PSEAE     1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYWRQTRGA 100
               SCOP domains d2h9dd_ D: Salicylate biosynthesis protein PchB                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CHORISMATE_MUT_2  PDB: D:4-94 UniProt: 4-94                                                ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2h9d D   1 MKTPEDCTGLADIREAIDRIDLDIVQALGRRMDYVKAASRFKASEAAIPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQIKYWRQTRGA 100
                                    10        20        30        40        50        60        70        80        90       100

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: All alpha proteins (14657)

Fold: Chorismate mutase II (21)

Superfamily: Chorismate mutase II (21)

Family: Dimeric chorismate mutase (10)

Protein domain: Salicylate biosynthesis protein PchB (2)

Pseudomonas aeruginosa [TaxId: 287] (2)

1a	d2h9da1	A:1-94
1b	d2h9db_	B:
1c	d2h9dc_	C:
1d	d2h9dd_	D:

(no "CATH Domain" information available for 2H9D)

(no "Pfam Domain" information available for 2H9D)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PCHB_PSEAE | Q51507)

molecular function
	GO:0016835	carbon-oxygen lyase activity	Catalysis of the breakage of a carbon-oxygen bond.
	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.
	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: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:0042864	pyochelin biosynthetic process	The chemical reactions and pathways resulting in the formation of the siderochrome pyochelin (2-(2-o-hydroxyphenyl-2-thiazolin-4-yl)-3-methylthiazolidine-4-carboxylic acid).
	GO:0009697	salicylic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of salicylic acid (2-hydroxybenzoic acid), a derivative of benzoic acid.

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	2h9d
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	4.1.99.-
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	PCHB_PSEAE \| Q51507	:	2h9c 3hgw 3hgx 3rem 3ret

Description

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Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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