2PW0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRANS-ACONITATE BOUND TO 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 :   1.57

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	TRC	2	Ligand/Ion	TRICARBALLYLIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	TRC	2	Ligand/Ion	TRICARBALLYLIC ACID

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	TRC	1	Ligand/Ion	TRICARBALLYLIC ACID

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	TRC	1	Ligand/Ion	TRICARBALLYLIC ACID

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	TRC	1	Ligand/Ion	TRICARBALLYLIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE B:144 , ASN B:219 , ALA B:220 , ILE B:222 , PRO B:223 , HOH B:2080 , HOH B:2159	BINDING SITE FOR RESIDUE EDO B 2045
2	AC2	SOFTWARE	ALA A:333 , GLU A:347 , LYS A:348 , GLU A:349 , GLN A:365 , ALA A:366 , TRP A:373	BINDING SITE FOR RESIDUE EDO A 2046
3	AC3	SOFTWARE	ASN A:219 , ALA A:220 , PRO A:223 , HOH A:2066 , HOH A:2124	BINDING SITE FOR RESIDUE EDO A 2047
4	AC4	SOFTWARE	GLU A:166 , ASP A:168 , ARG A:352 , HOH A:2193	BINDING SITE FOR RESIDUE EDO A 2048
5	AC5	SOFTWARE	PRO B:33 , GLU B:34 , HOH B:2112 , HOH B:2228	BINDING SITE FOR RESIDUE EDO B 2049
6	AC6	SOFTWARE	ALA B:333 , GLU B:347 , LYS B:348 , GLU B:349 , ALA B:364 , GLN B:365 , ALA B:366	BINDING SITE FOR RESIDUE EDO B 2050
7	AC7	SOFTWARE	SER A:22 , SER A:69 , SER A:70 , LYS A:73 , CYS A:107 , ASN A:109 , HIS A:278 , LYS A:281 , SER A:312 , MET A:313 , HIS A:317 , MET A:321 , GLY A:322 , HOH A:2511 , HOH A:2512 , HOH A:2513 , HOH A:2514	BINDING SITE FOR RESIDUE TRC A 2001
8	AC8	SOFTWARE	SER B:22 , SER B:69 , SER B:70 , LYS B:73 , ASN B:109 , LYS B:281 , HIS B:317 , MET B:321 , GLY B:322 , HOH B:2457 , HOH B:2459 , HOH B:2460 , HOH B:2461	BINDING SITE FOR RESIDUE TRC B 2002

(no "SS Bond" information available for 2PW0)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2PW0)

(no "PROSITE Motif" information available for 2PW0)

(no "Exon" information available for 2PW0)

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:386
 aligned with PRPF_SHEON | Q8EJW4 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:392
                                    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       355       365       375       385       395  
           PRPF_SHEON     6 FPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
               SCOP domains d2pw0a1 A:6-185 automated matches                                                                                                                                                   d2      pw0a2 A:186-397 automated matches                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeee.hhhhhhhh..hhhhhhhhhhhhh....................eeeeeee.......eeeeeeee......ee.......hhhhhhhhhhhh...hhhhh...eeeeeeeee....eeeeeeeeee..ee.................eeeeee.....------.........eeeee...eeeeeeeee...eeeeee.hhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhh....eeeeee....ee.....eehhhhh.eeeeeee..ee....hhhhhhhhhhhhh...hhhhhhh......eeeeee..eeeeeeeeeeee..eeeeeeeeeee.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw0 A   6 FPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAAD------CMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 397
                                    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       355       365       375       385       395  
                                                                                                                                                                                                               187    194

Chain B from PDB  Type:PROTEIN  Length:342
 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 d2pw0b1 B:5-185 automated matches                                                                                                                                                    d2      pw0b2 B:186        -397 automated matches                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeee.hhhhhhhh..hhhhhhhhhhhhh....................eeeeeee.......eeeeeeee......ee.......hhhhhhhhhhhh...hhhhh...eeeeeeeee....eeeeeeeeee..ee.................eeeeee.....------...........--------..eeeee...eeeeee.hhhh.....hhhhh...----------------------------------.eeeee....ee.....eehhhhh.eeeeee---......hhhhhhhhhhhhh...hhhhhhh......eeeeee..eeeeeeeeeeee..eeeeeeeeeee.eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pw0 B   5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAAD------CMFPTGNLVDV--------FNATMINAGIPTIFINAEDLGYTGTELQDDINSD----------------------------------KIAFVAPPKSYASSSGKTVAAEDVDLLVRAL---KLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP 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 |       -         -         -      |284       294       304      |  -|      324       334       344       354       364       374       384       394   
                                                                                                                                                                                                                187    194       204      213                              246                                281                           311 315

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) (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	d2pw0a1	A:6-185
1b	d2pw0a2	A:186-397
1c	d2pw0b1	B:5-185
1d	d2pw0b2	B:186-397

(no "CATH Domain" information available for 2PW0)

(no "Pfam Domain" information available for 2PW0)

Asymmetric 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 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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRC	[ 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 ]

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2pw0
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PRPF_SHEON \| Q8EJW4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PRPF_SHEON \| Q8EJW4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PRPF_SHEON \| Q8EJW4	:	2pvz 5k87

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

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