2C18 - JenaLib

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:2062 , HOH B:2172 , HOH B:2316	BINDING SITE FOR RESIDUE MG A 347
02	AC2	SOFTWARE	HOH A:2234 , HOH A:2238 , HOH A:2242 , HOH B:2305	BINDING SITE FOR RESIDUE MG A 348
03	AC3	SOFTWARE	HOH A:2303 , HOH A:2306 , HOH B:2033 , HOH B:2067	BINDING SITE FOR RESIDUE MG A 349
04	AC4	SOFTWARE	GLU A:245 , HOH A:2214 , HOH A:2218 , HOH A:2270 , HOH A:2272 , HOH A:2273	BINDING SITE FOR RESIDUE MG A1337
05	AC5	SOFTWARE	ASP A:131 , ASP A:139 , ASP A:176 , HOH A:2172 , HOH A:2176 , HOH A:2212	BINDING SITE FOR RESIDUE MG A1338
06	AC6	SOFTWARE	ASP A:37 , ASP A:319 , LEU B:27 , HOH B:2060 , HOH B:2065	BINDING SITE FOR RESIDUE NA A1339
07	AC7	SOFTWARE	SER A:175 , MET A:177 , LYS A:205 , TYR A:232 , GLN A:233 , HOH A:2176	BINDING SITE FOR RESIDUE CL A1340
08	AC8	SOFTWARE	TYR A:147 , ASN A:150 , HOH A:2081 , HOH A:2191	BINDING SITE FOR RESIDUE CL A1342
09	AC9	SOFTWARE	GLU B:245 , HOH B:2233 , HOH B:2234 , HOH B:2237 , HOH B:2276 , HOH B:2277	BINDING SITE FOR RESIDUE MG B1337
10	BC1	SOFTWARE	ASP B:131 , ASP B:139 , ASP B:176 , HOH B:2203 , HOH B:2229 , HOH B:2251	BINDING SITE FOR RESIDUE MG B1338
11	BC2	SOFTWARE	LEU A:27 , HOH A:2053 , HOH A:2058 , ASP B:37 , ASP B:319 , HOH B:2085	BINDING SITE FOR RESIDUE NA B1339
12	BC3	SOFTWARE	TYR A:10 , TYR A:12 , ARG A:14 , GLU B:187 , GLU B:190	BINDING SITE FOR RESIDUE PGE A1341
13	BC4	SOFTWARE	GLU A:187 , GLU A:190 , SER A:191 , TYR B:10 , TYR B:12 , ARG B:14 , HOH B:2325	BINDING SITE FOR RESIDUE PGE B1340

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:334
 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 d2c18a_ A: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2c18A00 A:3-336 Aldolase class I                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhh...............hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c18 A   3 FTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVkPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    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    
                                                                                                                                                                                                                                                                                           260-LSO

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    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     
           HEM2_PSEAE     2 SFTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
               SCOP domains d2c18b_ B: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2c18B00 B:2-336 Aldolase class I                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh..------hhhhh......hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c18 B   2 SFTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGSA------NKATYQMDPANSDEALHEVAADLAEGADMVMVkPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    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     
                                                                                                                                                                                                                                                     221    228                             260-LSO

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LSO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

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
2c16	5-(4-CARBOXY-2-OXO-BUTANE-1-SULFINYL)-4 -OXO-PENTANOIC ACID 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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (13, 13)