1GZG - JenaLib

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Title :   COMPLEX OF A MG2-DEPENDENT PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA (MUTANT D139N) WITH 5-FLUOROLEVULINIC ACID

Authors :   F. Frere, W. -D. Schubert, F. Stauffer, N. Frankenberg, R. Neier, D. Jahn, D. W. Heinz

Date :   21 May 02 (Deposition) - 27 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

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

Keywords :   Lyase, Heme Biosynthesis, 5-Fluorolevulinic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Frere, W. -D. Schubert, F. Stauffer, N. Frankenberg, R. Neier, D. Jahn, D. W. Heinz
Structure Of Porphobilinogen Synthase From Pseudomonas Aeruginosa In Complex With 5-Fluorolevulinic Acid Suggests A Double Schiff Base Mechanism
J. Mol. Biol. V. 320 237 2002
PubMed-ID: 12079382 | Reference-DOI: 10.1016/S0022-2836(02)00472-2

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	SCHIFF BASE LINKS BETWEEN ATOMS NZ OF LYS205 AND LYS260 AND ATOMS C5 OF 5-FLUOROLEVULINIC ACID
	Synonym	:	PORPHOBILINOGEN SYNTHASE, ALAD, ALADH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	LAF	5	Ligand/Ion	5-FLUOROLEVULINIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	NA	2	Ligand/Ion	SODIUM ION
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 28)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	LAF	20	Ligand/Ion	5-FLUOROLEVULINIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:181 , GLU A:245 , HOH A:2242 , HOH A:2243 , HOH A:2296 , HOH A:2297 , HOH A:2298	BINDING SITE FOR RESIDUE MG A1338
02	AC2	SOFTWARE	ASP A:127 , ALA A:129 , ASP A:131 , SER A:175 , LAF A:1336 , LAF A:1337 , HOH A:2196	BINDING SITE FOR RESIDUE NA A1339
03	AC3	SOFTWARE	PHE A:119 , PRO A:120 , GLU A:121 , LEU A:122 , HOH A:2354	BINDING SITE FOR RESIDUE SO4 A1340
04	AC4	SOFTWARE	ARG A:26 , LEU A:27 , HOH A:2047 , HOH A:2049 , ASP B:36 , ASP B:37 , ASP B:319	BINDING SITE FOR RESIDUE K B1339
05	AC5	SOFTWARE	ASP A:36 , ASP A:37 , ASP A:319 , ARG B:26 , LEU B:27 , HOH B:2066 , HOH B:2067	BINDING SITE FOR RESIDUE K B1340
06	AC6	SOFTWARE	GLU B:245 , ASP B:249 , HOH B:2219 , HOH B:2258 , HOH B:2259 , HOH B:2260 , HOH B:2261	BINDING SITE FOR RESIDUE MG B1341
07	AC7	SOFTWARE	ASP B:127 , SER B:175 , LAF B:1336 , LAF B:1337 , LAF B:1338 , HOH B:2194 , HOH B:2195	BINDING SITE FOR RESIDUE NA B1342
08	AC8	SOFTWARE	VAL B:76 , PHE B:119 , PRO B:120 , GLU B:121 , LEU B:122	BINDING SITE FOR RESIDUE SO4 B1343
09	AC9	SOFTWARE	ALA A:129 , ASP A:131 , ASN A:139 , SER A:175 , LYS A:205 , TYR A:211 , ARG A:215 , LYS A:229 , GLN A:233 , LYS A:260 , LAF A:1337 , NA A:1339 , HOH A:2195	BINDING SITE FOR RESIDUE LAF A1336
10	BC1	SOFTWARE	PHE A:86 , SER A:175 , LYS A:205 , TYR A:211 , PHE A:214 , LYS A:260 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324 , LAF A:1336 , NA A:1339	BINDING SITE FOR RESIDUE LAF A1337
11	BC2	SOFTWARE	SER B:175 , LYS B:205 , LYS B:229 , GLN B:233 , LYS B:260 , LAF B:1337 , LAF B:1338 , NA B:1342 , HOH B:2199 , HOH B:2316 , HOH B:2317	BINDING SITE FOR RESIDUE LAF B1336
12	BC3	SOFTWARE	SER B:175 , LYS B:205 , TYR B:211 , PHE B:214 , LYS B:260 , TYR B:283 , VAL B:285 , SER B:286 , TYR B:324 , LAF B:1336 , LAF B:1338 , NA B:1342	BINDING SITE FOR RESIDUE LAF B1337
13	BC4	SOFTWARE	ASP B:127 , ALA B:129 , ASP B:131 , SER B:175 , LYS B:205 , ARG B:215 , LYS B:229 , GLN B:233 , LYS B:260 , LAF B:1336 , LAF B:1337 , NA B:1342 , HOH B:2194 , HOH B:2195 , HOH B:2199 , HOH B:2315 , HOH B:2316 , HOH B:2317	BINDING SITE FOR RESIDUE LAF B1338

(no "SS Bond" information available for 1GZG)

Asymmetric Unit

No.	Residues
1	Tyr A:10	-	Pro A:11
2	Lys A:260	-	Pro A:261
3	Tyr B:10	-	Pro B:11
4	Lys B:260	-	Pro B:261

(no "SAP(SNP)/Variant" information available for 1GZG)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_ALA_DEHYDRATASE	PS00169	Delta-aminolevulinic acid dehydratase active site.	HEM2_PSEAE	253-265	2	A:253-265 B:253-265

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_ALA_DEHYDRATASE	PS00169	Delta-aminolevulinic acid dehydratase active site.	HEM2_PSEAE	253-265	8	A:253-265 B:253-265

(no "Exon" information available for 1GZG)

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:329
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:329
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326         
           HEM2_PSEAE     7 NRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
               SCOP domains d1gzga_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1gzgA00 A:7-335 Aldolase class I                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeeeeee..hhhhhhhhhhh.hhhhhh.............hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzg A   7 NRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQNGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:331
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
           HEM2_PSEAE     5 PANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
               SCOP domains d1gzgb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1gzgB00 B:5-335 Aldolase class I                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...........hhhhhhhhhhhhhh...eeeeee.hhhh...............hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhh.--------..........hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gzg B   5 PANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQNGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGS--------KATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     |   -    |  234       244       254       264       274       284       294       304       314       324       334 
                                                                                                                                                                                                                                                 220      229

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) (36)

Protein domain: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) (21)

Pseudomonas aeruginosa [TaxId: 287] (2)

1a	d1gzga_	A:
1b	d1gzgb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Pseudomonas aeruginosa. Organism_taxid: 287. (10)

1a	1gzgB00	B:5-335
1b	1gzgA00	A:7-335

(no "Pfam Domain" information available for 1GZG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEM2_PSEAE | Q59643)

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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004655	porphobilinogen synthase activity	Catalysis of the reaction: 2 5-aminolevulinate = 2 H(2)O + H(+) + porphobilinogen.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006783	heme biosynthetic process	The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
	GO:0006779	porphyrin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
	GO:0006782	protoporphyrinogen IX biosynthetic process	The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
	GO:0033014	tetrapyrrole biosynthetic process	The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
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.

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	Cis Peptide Bonds
		Lys A:260 - Pro A:261	[ RasMol ]
		Lys B:260 - Pro B:261	[ RasMol ]
		Tyr A:10 - Pro A:11	[ RasMol ]
		Tyr B:10 - Pro B:11	[ RasMol ]

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	1gzg
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1b4k	HIGH RESOLUTION CRYSTAL STRUCTURE OF A MG2- DEPENDENT 5- AMINOLEVULINIC ACID DEHYDRATASE

Description

Compounds

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Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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