2C16 - JenaLib

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Title :   5-(4-CARBOXY-2-OXO-BUTANE-1-SULFINYL)-4-OXO-PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA

Authors :   F. Frere, M. Nentwich, S. Gacond, D. W. Heinz, R. Neier, N. Frankenberg-Dinkel

Date :   11 Sep 05 (Deposition) - 20 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

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

Keywords :   Enzyme Mechanism, Metalloenzyme, Porphobilinogen Synthase, Cocrystallization, Lyase, Magnesium, Metal-Binding, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Frere, M. Nentwich, S. Gacond, D. W. Heinz, R. Neier, N. Frankenberg-Dinkel
Probing The Active Site Of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors.
Biochemistry V. 45 8243 2006
PubMed-ID: 16819823 | Reference-DOI: 10.1021/BI052611F

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
	Chains	:	A, B,
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET3A
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	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, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	OBS	2	Mod. Amino Acid	(Z)-N^6-[(4S,5R)-5-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-1-HYDROXYDIHYDRO-2H-THIOPYRANIUM-3(4H)-YLIDENE]-L-LYSINE
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	OBS	8	Mod. Amino Acid	(Z)-N^6-[(4S,5R)-5-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-1-HYDROXYDIHYDRO-2H-THIOPYRANIUM-3(4H)-YLIDENE]-L-LYSINE
4	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PGE	8	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:245 , HOH A:2234 , HOH A:2236 , HOH A:2277 , HOH A:2279 , HOH A:2280	BINDING SITE FOR RESIDUE MG A1336
2	AC2	SOFTWARE	ARG B:181 , GLU B:245 , HOH B:2225 , HOH B:2226 , HOH B:2264 , HOH B:2266 , HOH B:2267	BINDING SITE FOR RESIDUE MG B1336
3	AC3	SOFTWARE	HIS B:194 , THR B:195 , ASN B:196 , VAL B:197	BINDING SITE FOR RESIDUE CL B1337
4	AC4	SOFTWARE	ASP A:97 , VAL A:152 , PGE A:1338 , ASN B:49	BINDING SITE FOR RESIDUE PGE A1337
5	AC5	SOFTWARE	LEU A:142 , ASP A:143 , ASP A:144 , VAL A:152 , PGE A:1337	BINDING SITE FOR RESIDUE PGE A1338
6	AC6	SOFTWARE	GLY A:183 , GLU A:187 , ALA A:251 , HOH A:2333	BINDING SITE FOR RESIDUE PEG A1339
7	AC7	SOFTWARE	TYR A:12 , GLY B:183 , GLU B:187 , ALA B:251 , HOH B:2319	BINDING SITE FOR RESIDUE PEG B1338
8	AC8	SOFTWARE	ARG B:62 , ASP B:216 , GLY B:219	BINDING SITE FOR RESIDUE PEG B1339

(no "SS Bond" information available for 2C16)

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 2C16)

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 2C16)

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:327
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           HEM2_PSEAE     3 FTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
               SCOP domains d2c16a_ A: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2c16A00 A:3-336 Aldolase class I                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh.-------hhhhh......hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c16 A   3 FTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAkYASAYYGPFRDAVGS-------NKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  |    212       | -     | 232       242       252       262       272       282       292       302       312       322       332    
                                                                                                                                                                                                                                    205-OBS        220     228

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           HEM2_PSEAE     3 FTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
               SCOP domains d2c16b_ B: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2c16B00 B:3-336 Aldolase class I                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh.-------hhhhh......hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c16 B   3 FTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAkYASAYYGPFRDAVGS-------NKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  |    212       | -     | 232       242       252       262       272       282       292       302       312       322       332    
                                                                                                                                                                                                                                    205-OBS        220     228

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: automated matches (15)

Pseudomonas aeruginosa [TaxId: 287] (8)

1a	d2c16a_	A:
1b	d2c16b_	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	2c16A00	A:3-336
1b	2c16B00	B:3-336

(no "Pfam Domain" information available for 2C16)

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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	2c16
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	4.2.1.24
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1b4k	HIGH RESOLUTION CRYSTAL STRUCTURE OF A MG2- DEPENDENT 5- AMINOLEVULINIC ACID DEHYDRATASE
1gzg	COMPLEX OF A MG2-DEPENDENT PORPHOBILINOGEN SYNTHASE (MUTANT D139N) WITH 5-FLUOROLEVULINIC ACID
1w54	STEPWISE INTRODUCTION OF A ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA (MUTATION D139C)
1w56	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C AND D131C)
1w5m	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C AND D139C)
1w5n	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS D131C AND D139C)
1w5o	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C AND D139C)
1w5p	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C, D139C, P132E)
1w5q	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C, D139C, P132E, K229R)
2c13	5-HYDROXY-LEVULINIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c14	5-(4-CARBOXY-2-OXO-BUTYLAMINO)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c15	5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c18	5-(4-CARBOXY-2-OXO-BUTANE-1-SULFONYL)-4 -OXO-PENTANOIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c19	5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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