3PVR - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX WITH BENZOYL-COA

Authors :   M. Cygler, A. M. Grishin, Montreal-Kingston Bacterial Structural Initiative (Bsgi)

Date :   07 Dec 10 (Deposition) - 19 Jan 11 (Release) - 22 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Protein-Protein Complex, Ferretin-Like Fold, Bacterial Multicomponent Monooxygenase, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Grishin, E. Ajamian, L. Tao, L. Zhang, R. Menard, M. Cygler
Structural And Functional Studies Of The Escherichia Coli Phenylacetyl-Coa Monooxygenase Complex.
J. Biol. Chem. V. 286 10735 2011
PubMed-ID: 21247899 | Reference-DOI: 10.1074/JBC.M110.194423

Molecule 1 - PHENYLACETIC ACID DEGRADATION PROTEIN PAAA
	Chains	:	A
	EC Number	:	1.14.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSFDUET-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1388, JW1383, PAAA, YDBO
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511145
	Strain	:	K12 SUBSTR. MG1655
	Synonym	:	PHENYLACETYL-COA RING 1,2-EPOXIDASE PAAA

Molecule 2 - PHENYLACETIC ACID DEGRADATION PROTEIN PAAC
	Chains	:	B, C
	EC Number	:	1.14.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1390, JW1385, PAAC, YDBP
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511145
	Strain	:	K12 SUBSTR. MG1655
	Synonym	:	PHENYLACETYL-COA RING 1,2-EPOXIDASE PAAC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	BYC	1	Ligand/Ion	BENZOYL COENZYME A
2	GOL	7	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	BYC	2	Ligand/Ion	BENZOYL COENZYME A
2	GOL	12	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BYC	-1	Ligand/Ion	BENZOYL COENZYME A
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:33 , GLN A:34 , GLN A:37 , HIS A:38 , SER A:41 , GLU A:42 , LYS A:68 , GLU A:72 , LYS A:103 , TYR A:104 , SER A:105 , SER A:106 , PHE A:108 , ASP A:126 , ASN A:132 , TYR A:144 , MET A:193 , MET A:194 , PHE A:195 , GLY A:196 , PRO A:197 , SER A:202 , PRO A:203 , ASN A:204 , LYS A:214 , ASN A:218 , PHE A:264 , ILE A:268 , GOL A:312 , HOH A:357 , HOH A:360 , HOH A:379 , HOH A:381 , HOH A:399 , HOH A:415 , HOH A:420	BINDING SITE FOR RESIDUE BYC A 310
2	AC2	SOFTWARE	TYR B:7 , ARG B:10 , ASN B:14 , TRP B:103 , ASP B:176 , PRO B:188 , LYS B:221 , HOH B:353 , HOH B:373 , HOH B:389	BINDING SITE FOR RESIDUE GOL B 249
3	AC3	SOFTWARE	ASP C:66 , THR C:71 , GLN C:240 , PRO C:244 , GLY C:245 , HOH C:299 , HOH C:353 , HOH C:361 , HOH C:386	BINDING SITE FOR RESIDUE GOL C 249
4	AC4	SOFTWARE	TYR C:7 , ARG C:10 , LEU C:11 , ASN C:14 , TRP C:103 , ASP C:176 , PRO C:188 , LYS C:221 , HOH C:273 , HOH C:293	BINDING SITE FOR RESIDUE GOL C 250
5	AC5	SOFTWARE	GLU C:24 , HIS C:28 , ASN C:87 , GLY C:88	BINDING SITE FOR RESIDUE GOL C 251
6	AC6	SOFTWARE	ASN A:198 , ASP A:219 , ARG A:222 , PHE A:256 , GLY A:257 , GLU A:258 , TRP A:261 , HOH A:383 , HOH A:398	BINDING SITE FOR RESIDUE GOL A 311
7	AC7	SOFTWARE	ARG A:33 , BYC A:310 , HOH A:346 , HOH A:347 , HOH A:448	BINDING SITE FOR RESIDUE GOL A 312
8	AC8	SOFTWARE	TRP A:286 , THR A:290 , ARG A:293	BINDING SITE FOR RESIDUE GOL A 313

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

Asymmetric Unit

No.	Residues
1	Gln B:212	-	Glu B:213

Asymmetric Unit (2, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PAAC_ECOLI_001 *	N	160	D	PAAC_ECOLI	---	---	B/C	N	160	D
2	UniProt	VAR_PAAA_ECOLI_001 *	T	210	A	PAAA_ECOLI	---	---	A	T	210	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PAAC_ECOLI_001 *	N	160	D	PAAC_ECOLI	---	---	C	N	160	D
2	UniProt	VAR_PAAA_ECOLI_001 *	T	210	A	PAAA_ECOLI	---	---	A	T	210	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PAAC_ECOLI_001 *	N	160	D	PAAC_ECOLI	---	---	B	N	160	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3PVR)

(no "Exon" information available for 3PVR)

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:304
 aligned with PAAA_ECOLI | P76077 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:304
                              1                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298    
           PAAA_ECOLI     - --MTQEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRKAILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGVIGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQMLQDAINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTVPDPDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHAQK 302
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---PaaA_PaaC-3pvrA01 A:2-291                                                                                                                                                                                                                                                                         ----------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.........eee....eee....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pvr A  -1 MRSTQEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRKAILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGVIGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQMLQDAINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTVPDPDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHAQK 302
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with PAAC_ECOLI | P76079 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           PAAC_ECOLI     1 MNQLTAYTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDEDTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKAIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAVDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEM 236
               SCOP domains d3pvrb_ B: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh............hhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pvr B   1 SNQLTAYTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDEDTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKAIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAVDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEM 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with PAAC_ECOLI | P76079 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           PAAC_ECOLI     1 MNQLTAYTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDEDTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKAIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAVDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQRVLPGQQW 248
               SCOP domains d3pvrc_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PaaA_PaaC-3pvrC01 C:2-248                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) -PaaA_PaaC-3pvrC02 C:2-248                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............hhhhh....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pvr C   1 SNQLTAYTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDEDTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKAIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAVDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQRVLPGQQW 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ribonucleotide reductase-like (185)

Protein domain: automated matches (42)

Escherichia coli [TaxId: 511145] (6)

1a	d3pvrb_	B:
1b	d3pvrc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: PaaA_PaaC (10)

Escherichia coli (strain K12) (7)

1a	PaaA_PaaC-3pvrA01	A:2-291
1b	PaaA_PaaC-3pvrC01	C:2-248
1c	PaaA_PaaC-3pvrC02	C:2-248

Asymmetric Unit(hide GO term definitions)

Chain A (PAAA_ECOLI | P76077)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0097266	phenylacetyl-CoA 1,2-epoxidase activity	Catalysis of the reaction: phenylacetyl-CoA + H(+) + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP(+).
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0010124	phenylacetate catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylacetate.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,C (PAAC_ECOLI | P76079)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0010124	phenylacetate catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylacetate.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln B:212 - Glu B:213	[ RasMol ]

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

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Access by PDB/NDB ID
	3pvr
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	PAAA_ECOLI \| P76077
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	PAAC_ECOLI \| P76079
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	1.14.13.-
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	PAAA_ECOLI \| P76077
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UniProtKB/Swiss-Prot
	PAAA_ECOLI \| P76077	:	3pvt 3pvy 3pw1 3pw8 3pwq 4ii4
	PAAC_ECOLI \| P76079	:	1otk 3pvt 3pvy 3pw1 3pw8 3pwq 4ii4

3pvt	THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX WITH 3- HYDROXYBUTANOYL-COA
3pvy	THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX WITH COENZYME A
3pw1	THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX WITH PHENYLACETYL-COA
3pw8	THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX WITH ACETYL-COA
3pwq	THE PHENYLACETYL-COA MONOOXYGENASE PAAAC SUBCOMPLEX RELATED ID: PAAA_ECOLI RELATED DB: TARGETDB RELATED ID: PAAC_ECOLI RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 3)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (6, 8)

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Related Entries

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Related Entries Specified in the PDB File