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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF HP0315 FROM HELICOBACTER PYLORI AS A VAPD PROTEIN WITH AN ENDORIBONUCLEASE ACTIVITY

Authors :   A. R. Kwon, J. H. Kim, B. J. Lee

Date :   04 Nov 11 (Deposition) - 08 Feb 12 (Release) - 08 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Ferrodoxin-Like Fold, Virulence Associated Protein D, Ribonuclease, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Kwon, J. H. Kim, S. J. Park, K. Y. Lee, Y. H. Min, H. Im, I. Lee, K. Y. Lee, B. J. Lee
Structural And Biochemical Characterization Of Hp0315 From Helicobacter Pylori As A Vapd Protein With An Endoribonuclease Activity.
Nucleic Acids Res. 2012
PubMed-ID: 22241770 | Reference-DOI: 10.1093/NAR/GKR1305

Molecule 1 - IMMUNOGLOBULIN G-BINDING PROTEIN G, VIRULENCE-ASSOCIATED PROTEIN D
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HP_0315, SPG, VAPD
	Organism Scientific	:	STREPTOCOCCUS, HELICOBACTER PYLORI
	Organism Taxid	:	1320, 85962
	Other Details	:	THE FUSION PROTEIN OF N-TERMINAL TAGS (MSE)Q, THE RESIDUES 304-357 FROM IGG-BINDING PROTEIN G, LINKER GS, RESIDUES 1-94 FROM VAPD AND C-TERMINAL TAGS LEHHHHHH
	Strain	:	26695
	Synonym	:	IGG-BINDING PROTEIN G

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3UI3)

(no "SS Bond" information available for 3UI3)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:77	-	Pro A:78
2	Glu B:77	-	Pro B:78

(no "SAP(SNP)/Variant" information available for 3UI3)

(no "PROSITE Motif" information available for 3UI3)

(no "Exon" information available for 3UI3)

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:143
 aligned with SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:199
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493         
           SPG2_STRSG   304 YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEMVTEV 502
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.------........hhhhhhhhhhhhhhh.--.eeeeeehhh.eeeeee.-------------.eeeeeee---eh------------hhhhhhhh...hhh----hhhhhhhhhhhh.-------eeee..-.eeee....hhhh--hhhhhhhhhhhhhhhhhheeeeeeeee...ee------hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ui3 A   3 YKLIL------GETTTEAVDAATAEKVFKQYANDN--DGEWTYDDATKTFTVTEG-------------SmYALAFD---LK------------IEILKKEYGEPYNK----AYDDLRQELELLG-------FEWTQG-SVYVNYSKENTLA--QVYKAINKLSQIEWFKKSVRDIRAFKVEDFSD------FTEIVKSL 153
                                |    - |      22        32    |  |42        52    |    -        59     |  66|        -   |    74      |  - |      90   |     - |    |102       112|  |   120       130       140    |    - |       
                                7     14                     37 40               57            58|    65  66|           68           81   82          94      95  100 |         113  |                            145    146       
                                                                                                59-MSE     67                                                       101            114

Chain A from PDB  Type:PROTEIN  Length:143
 aligned with VAPD_HELPY | O05728 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:143
                                                                            1                                                                                           94 
                                     -         -         -         -        |2        12        22        32        42        52        62        72        82        92 | 
           VAPD_HELPY     - ------------------------------------------------MYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKS-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.........hhhhhhhhhhhhhhh..eeeeeehhh.eeeeee..eeeeeeeehhhhhhhhh...hhhhhhhhhhhhhhh.eeee...eeee....hhhhhhhhhhhhhhhhhhhhhheeeeeeeee...eehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ui3 A   3 YKLILGETTTEAVDAATAEKVFKQYANDNDGEWTYDDATKTFTVTEGSmYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKSL 153
                                ||  18        28        40        50        60        70        80        90       100       110       120       130       140       150   
                                7|                     37|                 59-MSE                                                                                          
                                14                      40

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:155
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     
           SPG2_STRSG    28 GSTVFAVDSPIEDTPIIRNGGELTNLLGNSETTLALRNEESATADLTAAAVADTVAAAAAENAGAAAWEAAAAADALAKAKADALKEFNKYGVSDYYKNLINNAKTVEGVKDLQAQVVESAKKARISEATDGLSDFLKSQTPAEDTVKSIELAEA 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhh.....h-----------hhhhhhhhhhhhh..eeee..eeee..-------------..hhhhhhhhhhhhhhhhhhhh---------hheeeeeeeeeee------------ee.hh-------hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ui3 B  56 EGSmYALAFDLKIEILKKEYGEPYN-----------KAYDDLRQELELLGFEWTQGSVYVNYS-------------KENTLAQVYKAINKLSQIEWFK---------KSVRDIRAFKVED------------FSDFT-------EIVKSLEHHHH 158
                               |    65        75    |    -      | 84        94       104  |      -      |111       121       | -       132       142         -  |   |  -    |  153     
                              59-MSE               80          81                       107           108                  129       130         142          143 147     148

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with VAPD_HELPY | O05728 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:103
                               1                                                                                           94      
                               |     7        17        27        37        47        57        67        77        87      |  -   
           VAPD_HELPY     - ---MYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKS------   -
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhh.....hhhhhhhhhhhhhh..eeee..eeee....hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3ui3 B  56 EGSmYALAFDLKIEILKKEYGEPYNKAYDDLRQELELLGFEWTQGSVYVNYSKENTLAQVYKAINKLSQIEWFKKSVRDIRAFKVEDFSDFTEIVKSLEHHHH 158
                               |    65        75        85        95       105       115       125       135       145       155   
                              59-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 3UI3)

(no "CATH Domain" information available for 3UI3)

(no "Pfam Domain" information available for 3UI3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SPG2_STRSG | P19909)

molecular function
	GO:0019864	IgG binding	Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
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.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B (VAPD_HELPY | O05728)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	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.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 3ui3)

	Cis Peptide Bonds
		Glu A:77 - Pro A:78	[ RasMol ]
		Glu B:77 - Pro B:78	[ RasMol ]

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Ligands, Modified Residues, Ions (1, 2)

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