2VY3 - JenaLib

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Title :   TYPE IV SECRETION SYSTEM EFFECTOR PROTEIN BEPA

Authors :   D. V. Palanivelu, T. Schirmer

Date :   17 Jul 08 (Deposition) - 17 Nov 09 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   T4Ss, Ob Fold, Fic Domain, Substrate Protein, Protein Translocation, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. V. Palanivelu, A. Goepfert, M. Meury, P. Guye, C. Dehio, T. Schirmer
Fic Domain Catalyzed Adenylylation: Insight Provided By The Structural Analysis Of The Type Iv Secretion System Effector Bepa.
Protein Sci. V. 20 492 2011
PubMed-ID: 21213248 | Reference-DOI: 10.1002/PRO.581

Molecule 1 - CELL FILAMENTATION PROTEIN
	Atcc	:	49882
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRUN
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Fragment	:	RESIDUES 1-302
	Organism Scientific	:	BARTONELLA HENSELAE
	Organism Taxid	:	38323
	Other Details	:	N-TERMINAL (HIS)6-TAG WITH THROMBIN CLEAVAGE SITE
	Synonym	:	BEPA PROTEIN, BEPA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	NI	4	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:17 , HIS A:18 , HOH A:2001 , HOH A:2002	BINDING SITE FOR RESIDUE NI A 501
2	AC2	SOFTWARE	HIS A:45 , LYS A:49 , HOH A:2003 , HOH A:2004 , HIS B:231	BINDING SITE FOR RESIDUE NI A 502
3	AC3	SOFTWARE	GLY A:164 , GLY A:166 , ARG A:167	BINDING SITE FOR RESIDUE CL A 601
4	AC4	SOFTWARE	HIS B:17 , HIS B:18 , HOH B:2001 , HOH B:2002	BINDING SITE FOR RESIDUE NI B 501
5	AC5	SOFTWARE	HIS A:231 , HIS B:45 , LYS B:49 , HOH B:2003	BINDING SITE FOR RESIDUE NI B 502
6	AC6	SOFTWARE	GLY B:164 , GLY B:166 , ARG B:167	BINDING SITE FOR RESIDUE CL B 601

(no "SS Bond" information available for 2VY3)

(no "Cis Peptide Bond" information available for 2VY3)

(no "SAP(SNP)/Variant" information available for 2VY3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	BEPA_BARHE	63-216	2	A:63-216 B:63-216

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	BEPA_BARHE	63-216	1	A:63-216 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	BEPA_BARHE	63-216	1	- B:63-216

(no "Exon" information available for 2VY3)

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:291
 aligned with BEPA_BARHE | Q6G2A9 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:291
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 
           BEPA_BARHE    12 EIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAMINLREESLPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGTTAAMPEMKRTGWKNAFAIGDEIQEGLQRLDQTLAEKNNLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERMMVASVAVAENGDLEPMQHLFEDISNPEKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETYTGTYRGAGLEGFALNVKGAYIIGNIDHLPPEQLKILKPGDKITFTAPK 302
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhh...............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.............ee.....ee................hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee.....eeeeeeeee...eeeee....eeeee.hhhhhhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------FIDO  PDB: A:63-216 UniProt: 63-216                                                                                                                       -------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vy3 A  12 EIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAmINLREESLPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGTTAAmPEmKRTGWKNAFAIGDEIQEGLQRLDQTLAEKNNLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERmmVASVAVAENGDLEPmQHLFEDISNPEKIRLLKEFmHTmKNTGRNVNDRPVmVAKEGETYTGTYRGAGLEGFALNVKGAYIIGNIDHLPPEQLKILKPGDKITFTAPK 302
                                    21        31        41        51        61        71        81        91       101  |    111       121       131       141       151       161       171       181       191  ||   201       211       221       231 |     241    |  251       261       271       281       291       301 
                                                                  51-MSE                                           101-MSE                                                                                      194-MSE         210-MSE             230-MSE         246-MSE                                                    
                                                                                                                      104-MSE                                                                                    195-MSE                               233-MSE

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with BEPA_BARHE | Q6G2A9 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:291
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 
           BEPA_BARHE    12 EIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAMINLREESLPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGTTAAMPEMKRTGWKNAFAIGDEIQEGLQRLDQTLAEKNNLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERMMVASVAVAENGDLEPMQHLFEDISNPEKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETYTGTYRGAGLEGFALNVKGAYIIGNIDHLPPEQLKILKPGDKITFTAPK 302
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.............ee.....ee.................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee.....eeeeee......eeeee....eeeee.hhhhhhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------FIDO  PDB: B:63-216 UniProt: 63-216                                                                                                                       -------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vy3 B  12 EIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAmINLREESLPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGTTAAmPEmKRTGWKNAFAIGDEIQEGLQRLDQTLAEKNNLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERmmVASVAVAENGDLEPmQHLFEDISNPEKIRLLKEFmHTmKNTGRNVNDRPVmVAKEGETYTGTYRGAGLEGFALNVKGAYIIGNIDHLPPEQLKILKPGDKITFTAPK 302
                                    21        31        41        51        61        71        81        91       101  |    111       121       131       141       151       161       171       181       191  ||   201       211       221       231 |     241    |  251       261       271       281       291       301 
                                                                  51-MSE                                           101-MSE                                                                                      194-MSE         210-MSE             230-MSE         246-MSE                                                    
                                                                                                                      104-MSE                                                                                    195-MSE                               233-MSE

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 2VY3)

(no "CATH Domain" information available for 2VY3)

(no "Pfam Domain" information available for 2VY3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BEPA_BARHE | Q6G2A9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0018117	protein adenylylation	The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid.
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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	Cis Peptide Bonds
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Biological Units
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	2vy3
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	BEPA_BARHE \| Q6G2A9	:	2jk8 2vza

(no "Related Entries Specified in the PDB File" available for 2VY3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (8, 8)

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