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Title :   CRYSTAL STRUCTURE OF FIC DOMAIN CONTAINING AMPYLATOR, VOPS

Authors :   P. H. Luong, L. N. Kinch, C. A. Brautigam, N. V. Grishin, D. R. Tomchick, K. Orth

Date :   15 Jan 10 (Deposition) - 21 Apr 10 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Ampylation, Fic Domain, Vibrio, Type Iii, Effector, T3Ss, Nucleotidyltransferase, Virulence, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. H. Luong, L. N. Kinch, C. A. Brautigam, N. V. Grishin, D. R. Tomchick, K. Orth
Structural And Kinetic Analysis Of Vops With Fic Domain Supports A Direct Transfer Mechanism For Ampylation
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE VOPS
	Chains	:	A, B
	EC Number	:	2.7.7.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEXTEV
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 75-387
	Gene	:	VOPS, VP 1686, VP1686
	Organism Scientific	:	VIBRIO PARAHAEMOLYTICUS
	Organism Taxid	:	670
	Strain	:	POR1
	Synonym	:	AMPYLATOR VOPS, VIBRIO OUTER PROTEIN S

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3LET)

(no "Site" information available for 3LET)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	VOPS_VIBPA	278-387	2	A:278-387 B:278-386

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	VOPS_VIBPA	278-387	1	A:278-387 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	VOPS_VIBPA	278-387	1	- B:278-386

(no "Exon" information available for 3LET)

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
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Chain A from PDB  Type:PROTEIN  Length:302
 aligned with VOPS_VIBPA | Q87P32 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:302
                                    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  
           VOPS_VIBPA    86 GQAQRLQTSSSVEHGQMLFKDANLKTPSDVLNAFAKLDSKMVKSHAAELSQLAERAMTEVMLETDSGKNLKALIGDDAVKSLAVRVVKDYGGGVAAAQKNPEVRINQMQAVFDMEVMHLKAAQRHIEGLASTDLNQGVYAEGLPEDAFNKAGVTNNVERAAAWIINASNSKGNDAENITSLLKEYATNGKDLLNMDNLKELHARLVPNVERDYRGPNISGGTLPSSIGGEGMLKQHIEGFLKENPVADKDLGKHLFAGVIGYHGFTDGNGRMGRMLYAIAELRNDSFNPLAMNAENSLHGIK 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FIDO  PDB: A:278-387 UniProt: 278-387                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3let A  86 GQAQRLQTSSSVEHGQMLFKDANLKTPSDVLNAFAKLDSKMVKSHAAELSQLAERAMTEVMLETDSGKNLKALIGDDAVKSLAVRVVKDYGGGVAAAQKNPEVRINQMQAVFDMEVMHLKAAQRHIEGLASTDLNQGVYAEGLPEDAFNKAGVTNNVERAAAWIINASNSKGNDAENITSLLKEYATNGKDLLNMDNLKELHARLVPNVERDYRGPNISGGTLPSSIGGEGMLKQHIEGFLKENPVADKDLGKHLFAGVIGYHGFTDGNGRMGRMLYAIAELRNDSFNPLAMNAENSLHGIK 387
                                    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

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with VOPS_VIBPA | Q87P32 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:310
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386
           VOPS_VIBPA    77 TKAVFDNEQGQAQRLQTSSSVEHGQMLFKDANLKTPSDVLNAFAKLDSKMVKSHAAELSQLAERAMTEVMLETDSGKNLKALIGDDAVKSLAVRVVKDYGGGVAAAQKNPEVRINQMQAVFDMEVMHLKAAQRHIEGLASTDLNQGVYAEGLPEDAFNKAGVTNNVERAAAWIINASNSKGNDAENITSLLKEYATNGKDLLNMDNLKELHARLVPNVERDYRGPNISGGTLPSSIGGEGMLKQHIEGFLKENPVADKDLGKHLFAGVIGYHGFTDGNGRMGRMLYAIAELRNDSFNPLAMNAENSLHGI 386
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Fic-3letB01 B:277-365                                                                    --------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Fic-3letB02 B:277-365                                                                    --------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FIDO  PDB: B:278-386 UniProt: 278-387                                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3let B  77 TKAVFDNEQGQAQRLQTSSSVEHGQMLFKDANLKTPSDVLNAFAKLDSKMVKSHAAELSQLAERAMTEVMLETDSGKNLKALIGDDAVKSLAVRVVKDYGGGVAAAQKNPEVRINQMQAVFDMEVMHLKAAQRHIEGLASTDLNQGVYAEGLPEDAFNKAGVTNNVERAAAWIINASNSKGNDAENITSLLKEYATNGKDLLNMDNLKELHARLVPNVERDYRGPNISGGTLPSSIGGEGMLKQHIEGFLKENPVADKDLGKHLFAGVIGYHGFTDGNGRMGRMLYAIAELRNDSFNPLAMNAENSLHGI 386
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

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 '\|'

(no "SCOP Domain" information available for 3LET)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Fic] (3)

Family: Fic (3)

Vibrio parahaemolyticus (1)

1a	Fic-3letB01	B:277-365
1b	Fic-3letB02	B:277-365

Asymmetric Unit(hide GO term definitions)

Chain A,B (VOPS_VIBPA | Q87P32)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0070733	protein adenylyltransferase activity	Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:0035024	negative regulation of Rho protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0018178	peptidyl-threonine adenylylation	The adenylylation of peptidyl-threonine to form peptidyl-O-(phospho-5'-adenosine)-L-threonine.
	GO:0018117	protein adenylylation	The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0044054	rounding by symbiont of host cells	Any process in which an organism causes host cells to change shape and become round.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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