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Title :   CRYSTAL STRUCTURE OF UROPORPHYRINOGEN DECARBOXYLASE FROM BACILLUS SUBTILIS

Authors :   J. Fan, Q. Liu, Q. Hao, M. K. Teng, L. W. Niu

Date :   06 Oct 06 (Deposition) - 24 Oct 06 (Release) - 17 Jun 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   (Alpha-Beta)8 Barrel, Eight Parallel Beta Strands Surrounded By Eight Alpha Helices, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Fan, Q. Liu, Q. Hao, M. K. Teng, L. W. Niu
Crystal Structure Of Uroporphyrinogen Decarboxylase From Bacillus Subtilis
J. Bacteriol. V. 189 3573 2007
PubMed-ID: 17122346 | Reference-DOI: 10.1128/JB.01083-06
(for further references see the PDB file header)

Molecule 1 - UROPORPHYRINOGEN DECARBOXYLASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	URO-D, UPD

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2INF)

(no "Site" information available for 2INF)

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UROD_1	PS00906	Uroporphyrinogen decarboxylase signature 1.	DCUP_BACSU	24-33	4	A:24-33 B:24-33 C:24-33 D:24-33
2	UROD_2	PS00907	Uroporphyrinogen decarboxylase signature 2.	DCUP_BACSU	142-158	4	A:142-158 B:142-158 C:142-158 D:142-158

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UROD_1	PS00906	Uroporphyrinogen decarboxylase signature 1.	DCUP_BACSU	24-33	2	A:24-33 B:24-33 - -
2	UROD_2	PS00907	Uroporphyrinogen decarboxylase signature 2.	DCUP_BACSU	142-158	2	A:142-158 B:142-158 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UROD_1	PS00906	Uroporphyrinogen decarboxylase signature 1.	DCUP_BACSU	24-33	2	- - C:24-33 D:24-33
2	UROD_2	PS00907	Uroporphyrinogen decarboxylase signature 2.	DCUP_BACSU	142-158	2	- - C:142-158 D:142-158

(no "Exon" information available for 2INF)

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:344
 aligned with DCUP_BACSU | P32395 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:344
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    
           DCUP_BACSU     6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMIEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIEAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
               SCOP domains d2infa_ A: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2infA00 A:6-349  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhh..ee.......ee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh....eee.....hhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------UROD_1    ------------------------------------------------------------------------------------------------------------UROD_2           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2inf A   6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMTEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIKAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with DCUP_BACSU | P32395 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:344
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    
           DCUP_BACSU     6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMIEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIEAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
               SCOP domains d2infb_ B: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2infB00 B:6-349  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...ee........hhhhh..................hhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhh....eee.....hhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------UROD_1    ------------------------------------------------------------------------------------------------------------UROD_2           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2inf B   6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMTEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIKAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain C from PDB  Type:PROTEIN  Length:344
 aligned with DCUP_BACSU | P32395 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:344
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    
           DCUP_BACSU     6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMIEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIEAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
               SCOP domains d2infc_ C: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2infC00 C:6-349  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...ee.......hhhhhh..eee.....eee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhh...eee.....hhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------UROD_1    ------------------------------------------------------------------------------------------------------------UROD_2           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2inf C   6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMTEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIKAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain D from PDB  Type:PROTEIN  Length:344
 aligned with DCUP_BACSU | P32395 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:344
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345    
           DCUP_BACSU     6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMIEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIEAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
               SCOP domains d2infd_ D: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2infD00 D:6-349  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...ee........hhhhh..................hhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh...eee.....hhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------UROD_1    ------------------------------------------------------------------------------------------------------------UROD_2           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2inf D   6 TFNETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKYGLFEITHQPELCAYVTRLPVEQYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPYVLETIKLLVNEQLNVPLIGFSGAPFTLASYMTEGGPSKNYNKTKAFMYSMPDAWNLLMSKLADMIIVYVKAQIKAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSELAKENVPLIMFGVGASHLAGDWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVIEQKTKEILDQGMESDGFIFNLGHGVFPDVSPEVLKKLTAFVHEYSQNKKM 349
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: UROD/MetE-like (30)

Family: automated matches (4)

Protein domain: automated matches (4)

Bacillus subtilis [TaxId: 1423] (1)

1a	d2infa_	A:
1b	d2infb_	B:
1c	d2infc_	C:
1d	d2infd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: [code=3.20.20.210, no name defined] (35)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	2infA00	A:6-349
1b	2infB00	B:6-349
1c	2infC00	C:6-349
1d	2infD00	D:6-349

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DCUP_BACSU | P32395)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0004853	uroporphyrinogen decarboxylase activity	Catalysis of the reaction: uroporphyrinogen-III = coproporphyrinogen + 4 CO2.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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