2Q2N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH DEUTEROPORPHYRIN IX 2,4-DISULFONIC ACID DIHYDROCHLORIDE

Authors :   T. Karlberg, O. H. Thorvaldsen, S. Al-Karadaghi

Date :   29 May 07 (Deposition) - 22 Apr 08 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Rossmann Fold; Pi-Helix, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Karlberg, M. D. Hansson, R. K. Yengo, R. Johansson, O. H. Thorvaldsen, G. C. Ferreira, M. Hansson, S. Al-Karadaghi
Porphyrin Binding And Distortion And Substrate Specificity In The Ferrochelatase Reaction: The Role Of Active Site Residues
J. Mol. Biol. V. 378 1074 2008
PubMed-ID: 18423489 | Reference-DOI: 10.1016/J.JMB.2008.03.040

Molecule 1 - FERROCHELATASE
	Chains	:	A
	EC Number	:	4.99.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HEMH, HEMF
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	PROTOHEME FERRO-LYASE; HEME SYNTHETASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	H01	1	Ligand/Ion	PROTOPORPHYRIN IX 2,4-DISULFONIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:9002 , HOH A:9003 , HOH A:9004 , HOH A:9005 , HOH A:9006 , HOH A:9007	BINDING SITE FOR RESIDUE MG A 1000
2	AC2	SOFTWARE	HOH A:9008 , HOH A:9009 , HOH A:9010 , HOH A:9011 , HOH A:9012 , HOH A:9013	BINDING SITE FOR RESIDUE MG A 2000
3	AC3	SOFTWARE	TYR A:13 , ILE A:29 , ARG A:30 , ARG A:31 , ARG A:33 , MET A:39 , PHE A:120 , HIS A:183 , SER A:184 , LEU A:185 , PRO A:195 , GLN A:199 , GLY A:224 , ASN A:225 , THR A:226 , PRO A:227 , TRP A:230 , HOH A:9032 , HOH A:9068 , HOH A:9093 , HOH A:9127 , HOH A:9181	BINDING SITE FOR RESIDUE H01 A 9001

(no "SS Bond" information available for 2Q2N)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:90	-	Pro A:91
2	Pro A:229	-	Trp A:230
3	Gly A:232	-	Pro A:233

(no "SAP(SNP)/Variant" information available for 2Q2N)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERROCHELATASE	PS00534	Ferrochelatase signature.	HEMH_BACSU	178-196	1	A:178-196

(no "Exon" information available for 2Q2N)

Asymmetric/Biological 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:309
 aligned with HEMH_BACSU | P32396 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
           HEMH_BACSU     2 SRKKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
               SCOP domains d2q2na_ A: Ferrochelatase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -2q2nA01 A:3-147,A:290-310  [code=3.40.50.1400, no name defined]                                                                                  2q2nA02 A:148-289  [code=3.40.50.1400, no name defined]                                                                                       2q2nA01               CATH domains
               Pfam domains ---Ferrochelatase-2q2nA01 A:5-308                                                                                                                                                                                                                                                                                  -- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhh..eeeee.......hhhhhh...hhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FERROCHELATASE     ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2n A   2 SRKKMGLLVMAYGTPYKEEDIERYYTHIRRGRKPEPEMLQDLKDRYEAIGGISPLAQITEQQAHNLEQHLNEIQDEITFKAYIGLKHIEPFIEDAVAEMHKDGITEAVSIVLAPHFSTFSVQSYNKRAKEEAEKLGGLTITSVESWYDEPKFVTYWVDRVKETYASMPEDERENAMLIVSAHSLPEKIKEFGDPYPDQLHESAKLIAEGAGVSEYAVGWQSEGNTPDPWLGPDVQDLTRDLFEQKGYQAFVYVPVGFVADHLEVLYDNDYECKVVTDDIGASYYRPEMPNAKPEFIDALATVVLKKLGR 310
                                    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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Chelatase-like (149)

Superfamily: Chelatase (46)

Family: Ferrochelatase (37)

Protein domain: Ferrochelatase (34)

Bacillus subtilis [TaxId: 1423] (15)

d2q2na_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1400, no name defined] (36)

Bacillus subtilis. Organism_taxid: 1423. (9)

1a	2q2nA01	A:3-147,A:290-310
1b	2q2nA02	A:148-289

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Chelatase (20)

Family: Ferrochelatase (12)

Bacillus subtilis (4)

Ferrochelatase-2q2nA01

A:5-308

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HEMH_BACSU | P32396)

molecular function
	GO:0004325	ferrochelatase activity	Catalysis of the reaction: protoheme = Fe(2+) + protoporphyrin IX.
	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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:90 - Pro A:91	[ RasMol ]
		Gly A:232 - Pro A:233	[ RasMol ]
		Pro A:229 - Trp A:230	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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