3RU6 - JenaLib

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Title :   1.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (PYRF) FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168

Authors :   A. S. Halavaty, G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Pa W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)

Date :   04 May 11 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Csgid), Tim-Barrel, Orotidine 5'-Phosphate To Ump And Carbon Dioxide Conversion, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Halavaty, G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 8 Angstrom Resolution Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase (Pyrf) From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
To Be Published
PubMed: search

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21/MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CJ0381C, PYRF
	Organism Scientific	:	CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
	Organism Taxid	:	192222
	Strain	:	NCTC 11168
	Synonym	:	OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 30)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	IOD	26	Ligand/Ion	IODIDE ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IOD	12	Ligand/Ion	IODIDE ION

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IOD	14	Ligand/Ion	IODIDE ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:91 , ASN D:123 , HOH D:352	BINDING SITE FOR RESIDUE CL A 280
02	AC2	SOFTWARE	LEU A:59 , LEU D:59	BINDING SITE FOR RESIDUE IOD A 281
03	AC3	SOFTWARE	LYS A:103 , ARG A:207	BINDING SITE FOR RESIDUE IOD A 282
04	AC4	SOFTWARE	GLY A:175	BINDING SITE FOR RESIDUE IOD A 284
05	AC5	SOFTWARE	THR A:117	BINDING SITE FOR RESIDUE IOD A 285
06	AC6	SOFTWARE	ARG A:100 , LYS A:103	BINDING SITE FOR RESIDUE IOD A 286
07	AC7	SOFTWARE	PHE A:179	BINDING SITE FOR RESIDUE IOD A 287
08	AC8	SOFTWARE	THR B:117	BINDING SITE FOR RESIDUE IOD B 280
09	AC9	SOFTWARE	PHE B:179	BINDING SITE FOR RESIDUE IOD B 281
10	BC1	SOFTWARE	ARG B:100 , LYS B:103 , ARG B:207	BINDING SITE FOR RESIDUE IOD B 282
11	BC2	SOFTWARE	LEU B:59 , LEU C:59	BINDING SITE FOR RESIDUE IOD B 283
12	BC3	SOFTWARE	LYS B:103 , ARG B:207	BINDING SITE FOR RESIDUE IOD B 284
13	BC4	SOFTWARE	GLY B:175	BINDING SITE FOR RESIDUE IOD B 285
14	BC5	SOFTWARE	ARG B:196	BINDING SITE FOR RESIDUE IOD B 286
15	BC6	SOFTWARE	LYS B:12 , LYS B:42 , GLU B:46	BINDING SITE FOR RESIDUE IOD B 287
16	BC7	SOFTWARE	ASN B:123 , HOH B:292 , LYS C:91	BINDING SITE FOR RESIDUE CL C 280
17	BC8	SOFTWARE	GLY B:90 , LYS B:91 , ASN C:123 , SER C:126 , HOH C:303	BINDING SITE FOR RESIDUE CL C 281
18	BC9	SOFTWARE	THR C:117 , HOH C:366	BINDING SITE FOR RESIDUE IOD C 282
19	CC1	SOFTWARE	GLY C:175	BINDING SITE FOR RESIDUE IOD C 283
20	CC2	SOFTWARE	ARG C:100 , LYS C:103	BINDING SITE FOR RESIDUE IOD C 286
21	CC3	SOFTWARE	LYS C:12	BINDING SITE FOR RESIDUE IOD C 287
22	CC4	SOFTWARE	ALA D:193 , ARG D:196 , LYS D:225	BINDING SITE FOR RESIDUE CL D 280
23	CC5	SOFTWARE	GLY D:175	BINDING SITE FOR RESIDUE IOD D 281
24	CC6	SOFTWARE	ARG D:100 , LYS D:103	BINDING SITE FOR RESIDUE IOD D 282
25	CC7	SOFTWARE	ARG D:177 , PHE D:179	BINDING SITE FOR RESIDUE IOD D 283
26	CC8	SOFTWARE	LYS D:103 , ARG D:177	BINDING SITE FOR RESIDUE IOD D 284
27	CC9	SOFTWARE	THR D:117 , HOH D:342	BINDING SITE FOR RESIDUE IOD D 285

(no "SS Bond" information available for 3RU6)

(no "Cis Peptide Bond" information available for 3RU6)

(no "SAP(SNP)/Variant" information available for 3RU6)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_CAMJE	55-68	4	A:55-68 B:55-68 C:55-68 D:55-68

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_CAMJE	55-68	2	A:55-68 - - D:55-68

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPDECASE	PS00156	Orotidine 5'-phosphate decarboxylase active site.	PYRF_CAMJE	55-68	2	- B:55-68 C:55-68 -

(no "Exon" information available for 3RU6)

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:220
 aligned with PYRF_CAMJE | Q9PIC1 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:228
                             1                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
           PYRF_CAMJE     - -MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFGETNDDQKRVANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
               SCOP domains d3ru6a_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh......eeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhh...eee....hhhhhhhhh....eeee.......--------..hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ru6 A   0 AMKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFG--------VANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179|      189       199       209       219        
                                                                                                                                                                                                              180      189

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with PYRF_CAMJE | Q9PIC1 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:228
                             1                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
           PYRF_CAMJE     - -MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFGETNDDQKRVANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
               SCOP domains d3ru6b_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh......eeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhh...eee....hhhhhhhhh....eeee.........------..hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ru6 B   0 AMKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFGET------VANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179  |    189       199       209       219        
                                                                                                                                                                                                                182    189

Chain C from PDB  Type:PROTEIN  Length:218
 aligned with PYRF_CAMJE | Q9PIC1 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           PYRF_CAMJE     1 MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFGETNDDQKRVANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
               SCOP domains d3ru6c_ C: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh......eeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhh...eee....hhhhhhhhh....eeee.......---------.hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ru6 C   1 MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFG---------ANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKIH 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
                                                                                                                                                                                                             180       190

Chain D from PDB  Type:PROTEIN  Length:218
 aligned with PYRF_CAMJE | Q9PIC1 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           PYRF_CAMJE     1 MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFGETNDDQKRVANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKI 226
               SCOP domains d3ru6d_ D: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) OMPdecase-3ru6D01 D:1-222                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) OMPdecase-3ru6D02 D:1-222                                                                                                                                                                                                     ---- Pfam domains (2)
           Pfam domains (3) OMPdecase-3ru6D03 D:1-222                                                                                                                                                                                                     ---- Pfam domains (3)
           Pfam domains (4) OMPdecase-3ru6D04 D:1-222                                                                                                                                                                                                     ---- Pfam domains (4)
         Sec.struct. author .eeeee....hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh......eeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhh...eee....hhhhhhhhh....eeee.......--------..hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------OMPDECASE     -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ru6 D   1 MKLCVALDLSTKEECLQLAKELKNLDIWLKVGLRAYLRDGFKFIEELKKVDDFKIFLDLKFHDIPNTMADACEEVSKLGVDMINIHASAGKIAIQEVMTRLSKFSKRPLVLAVSALTSFDEENFFSIYRQKIEEAVINFSKISYENGLDGMVCSVFESKKIKEHTSSNFLTLTPGIRPFG--------VANLAMARENLSDYIVVGRPIYKNENPRAVCEKILNKI 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                                                                                                                                                                             180      189

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: automated matches (38)

Protein domain: automated matches (38)

Campylobacter jejuni [TaxId: 192222] (3)

1a	d3ru6a_	A:
1b	d3ru6b_	B:
1c	d3ru6c_	C:
1d	d3ru6d_	D:

(no "CATH Domain" information available for 3RU6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: OMPdecase (84)

Campylobacter jejuni (1)

1a	OMPdecase-3ru6D01	D:1-222
1b	OMPdecase-3ru6D02	D:1-222
1c	OMPdecase-3ru6D03	D:1-222
1d	OMPdecase-3ru6D04	D:1-222

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PYRF_CAMJE | Q9PIC1)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0004590	orotidine-5'-phosphate decarboxylase activity	Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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	3ru6
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 30)

Sites (27, 27)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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