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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF METHYLACONITATE ISOMERASE PRPF FROM SHEWANELLA ONEIDENSIS

Authors :   G. S. Garvey, I. R. Rayment

Date :   10 May 07 (Deposition) - 21 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

Chains :   Asym./Biol. Unit : A,B

Keywords :   Propionate Catabolism, Diaminopimelate Epimerase Like, Aconitate Binding, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. S. Garvey, C. J. Rocco, J. C. Escalante-Semerena, I. Rayment
The Three-Dimensional Crystal Structure Of The Prpf Protein Of Shewanella Oneidensis Complexed With Trans-Aconitate: Insights Into Its Biological Function.
Protein Sci. V. 16 1274 2007
PubMed-ID: 17567742 | Reference-DOI: 10.1110/PS.072801907

Molecule 1 - PRPF METHYLACONITATE ISOMERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PPRP196
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PRPF
	Organism Scientific	:	SHEWANELLA ONEIDENSIS
	Organism Taxid	:	70863

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:240 , LYS B:59	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	LYS A:59 , GLN B:240	BINDING SITE FOR RESIDUE CA A 1002
3	AC3	SOFTWARE	SER A:69 , LYS A:73 , SER A:312 , HIS A:317	BINDING SITE FOR RESIDUE CA A 1003
4	AC4	SOFTWARE	LEU A:29 , GLN A:30 , HOH A:1186 , HOH A:1364	BINDING SITE FOR RESIDUE CA A 1004
5	AC5	SOFTWARE	SER A:22 , CSD A:107 , GLY A:108 , ASN A:109 , MET A:321 , GLY A:322 , THR A:323	BINDING SITE FOR RESIDUE EDO A 1005
6	AC6	SOFTWARE	ALA A:13 , ALA A:14 , THR A:15 , PHE A:117 , ASN A:121 , HOH A:1081 , HOH A:1090 , HOH A:1360	BINDING SITE FOR RESIDUE EDO A 1007
7	AC7	SOFTWARE	PRO A:184 , ASN A:219 , GLY A:221 , HOH A:1085	BINDING SITE FOR RESIDUE EDO A 1010
8	AC8	SOFTWARE	LEU A:250 , PHE A:253 , GLU A:254 , ARG A:257 , ILE A:282 , LEU A:311 , MET A:313 , GLY A:314 , HOH A:1111 , HOH A:1113 , HOH A:1123	BINDING SITE FOR RESIDUE EDO A 1011

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:53	-	Pro A:54
2	Thr A:279	-	Pro A:280
3	Ser B:53	-	Pro B:54
4	Thr B:279	-	Pro B:280

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

(no "PROSITE Motif" information available for 2PVZ)

(no "Exon" information available for 2PVZ)

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:387
 aligned with PRPF_SHEON | Q8EJW4 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
           PRPF_SHEON     5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
               SCOP domains d2pvza1 A:5-185 automated matches                                                                                                                                                    d2      pvza2 A:186-397 automated matches                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeee.hhhhhhhhh.hhhhhhhhhhhhh...............hhhh.eeeeeee.......eeeeeeee......ee.......hhhhhhhhhhhh...hhhhh...eeeeeeeee....eeeeeeeeee..ee.................eeeeee.....------.........eeeee...eeeeeeeee...eeeeee.hhhh.....hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhh....eeeeee....ee.....eehhhhh.eeeeeee..ee....hhhhhhhhhhhhhh..hhhhhhh......eeeeee..eeeeee..eeee..eeee.eeeeee.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvz A   5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNcGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAAD------CMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
                                    14        24        34        44        54        64        74        84        94       104  |    114       124       134       144       154       164       174       184  |    194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
                                                                                                                                107-CSD                                                                         187    194

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with PRPF_SHEON | Q8EJW4 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
           PRPF_SHEON     5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
               SCOP domains d2pvzb1 B:5-185 automated matches                                                                                                                                                    d2      pvzb2 B:186-397 automated matches                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeee.hhhhhhhhh.hhhhhhhhhhhhh...............hhhh.eeeeeee.......eeeeeeee......ee.......hhhhhhhhhhhh...hhhhh...eeeeeeeee....eeeeeeeeee..ee.................eeeeee.....------.........eeeee...eeeeeeeee...eeeeee.hhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhh.....eeeeee....ee.....eehhhhh.eeeeeee..ee....hhhhhhhhhhhhh...hhhhhhh......eeeeee..eeeeeeeeeeee..eeeeeeeeeee.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvz B   5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNcGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAAD------CMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
                                    14        24        34        44        54        64        74        84        94       104  |    114       124       134       144       154       164       174       184  |    194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
                                                                                                                                107-CSD                                                                         187    194

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) (23004)

Fold: Diaminopimelate epimerase-like (37)

Superfamily: Diaminopimelate epimerase-like (37)

Family: automated matches (15)

Protein domain: automated matches (15)

Shewanella oneidensis [TaxId: 70863] (2)

1a	d2pvza1	A:5-185
1b	d2pvza2	A:186-397
1c	d2pvzb1	B:5-185
1d	d2pvzb2	B:186-397

(no "CATH Domain" information available for 2PVZ)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PRPF_SHEON | Q8EJW4)

molecular function
	GO:0016863	intramolecular oxidoreductase activity, transposing C=C bonds	Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, one or more carbon-carbon double bonds in the molecule are rearranged, and no oxidized product appears.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0019629	propionate catabolic process, 2-methylcitrate cycle	The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:53 - Pro A:54	[ RasMol ]
		Ser B:53 - Pro B:54	[ RasMol ]
		Thr A:279 - Pro A:280	[ RasMol ]
		Thr B:279 - Pro B:280	[ RasMol ]

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	2pvz
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	PRPF_SHEON \| Q8EJW4	:	2pw0 5k87

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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