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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF UREE FROM HELICOBACTER PYLORI (NI2+ BOUND FORM)

Authors :   R. Shi, C. Munger, A. Assinas, A. Matte, M. Cygler, Montreal-Kingston Structural Genomics Initiative (Bsgi)

Date :   14 Jul 10 (Deposition) - 25 Aug 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.09

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

Keywords :   Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Urease Maturation Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Shi, C. Munger, A. Asinas, S. L. Benoit, E. Miller, A. Matte, R. J. Maier, M. Cygler
Crystal Structures Of Apo And Metal-Bound Forms Of The Uree Protein From Helicobacter Pylori: Role Of Multiple Metal Binding Sites
Biochemistry V. 49 7080 2010
PubMed-ID: 20681615 | Reference-DOI: 10.1021/BI100372H

Molecule 1 - UREASE ACCESSORY PROTEIN UREE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HP_0070, UREE
	Organism Common	:	CAMPYLOBACTER PYLORI
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Strain	:	ATCC 43504

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:102 , HIS B:102 , HIS B:152 , HIS C:102 , HIS D:102	BINDING SITE FOR RESIDUE NI B 171

(no "SS Bond" information available for 3NY0)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:16	-	Asp A:17
2	Leu B:13	-	Asn B:14
3	Leu B:16	-	Asp B:17
4	Val B:148	-	Ser B:149
5	Leu C:13	-	Asn C:14
6	Leu C:16	-	Asp C:17
7	Leu D:13	-	Asn D:14
8	Leu D:16	-	Asp D:17

(no "SAP(SNP)/Variant" information available for 3NY0)

(no "PROSITE Motif" information available for 3NY0)

(no "Exon" information available for 3NY0)

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:147
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           UREE_HELPY     2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee....eeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh..eeee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ny0 A   2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
           UREE_HELPY     2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee..eeehhhhh...eeeee.....eeeee.............eeee...eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhh.....eeee..hhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ny0 B   2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
           UREE_HELPY     2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeehhhhhh..............................eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhh.....ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ny0 C   2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
           UREE_HELPY     2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----UreE_N-3ny0D05 D:6-71                                             -----UreE_C-3ny0D01 D:77-149                                                   Pfam domains (1)
           Pfam domains (2) ----UreE_N-3ny0D06 D:6-71                                             -----UreE_C-3ny0D02 D:77-149                                                   Pfam domains (2)
           Pfam domains (3) ----UreE_N-3ny0D07 D:6-71                                             -----UreE_C-3ny0D03 D:77-149                                                   Pfam domains (3)
           Pfam domains (4) ----UreE_N-3ny0D08 D:6-71                                             -----UreE_C-3ny0D04 D:77-149                                                   Pfam domains (4)
         Sec.struct. author ..................eeeeee..hhhhh...eee.....eee.................eee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhh...eeeeeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ny0 D   2 IIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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 3NY0)

(no "CATH Domain" information available for 3NY0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: UreE_C] (4)

Family: UreE_C (4)

Helicobacter pylori (Campylobacter pylori) (4)

1a	UreE_C-3ny0D01	D:77-149
1b	UreE_C-3ny0D02	D:77-149
1c	UreE_C-3ny0D03	D:77-149
1d	UreE_C-3ny0D04	D:77-149

Clan: no clan defined [family: UreE_N] (4)

Family: UreE_N (4)

Helicobacter pylori (Campylobacter pylori) (4)

2a	UreE_N-3ny0D05	D:6-71
2b	UreE_N-3ny0D06	D:6-71
2c	UreE_N-3ny0D07	D:6-71
2d	UreE_N-3ny0D08	D:6-71

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (UREE_HELPY | Q09064)

molecular function
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	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).
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0018307	enzyme active site formation	The modification of part of an enzyme to form the active site.
	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:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0019627	urea metabolic process	The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:16 - Asp A:17	[ RasMol ]
		Leu B:13 - Asn B:14	[ RasMol ]
		Leu B:16 - Asp B:17	[ RasMol ]
		Leu C:13 - Asn C:14	[ RasMol ]
		Leu C:16 - Asp C:17	[ RasMol ]
		Leu D:13 - Asn D:14	[ RasMol ]
		Leu D:16 - Asp D:17	[ RasMol ]
		Val B:148 - Ser B:149	[ RasMol ]

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	UREE_HELPY \| Q09064	:	3l9z 3la0 3nxz 3tj8 3tj9 3tja

3l9z	CRYSTAL STRUCTURE OF APO FORM OF H. PYROLI UREE
3la0	CRYSTAL STRUCTURE OF METAL (UNKNOWN IDENTITY) BOUND FORM OF H. PYROLI UREE
3nxz	CRYSTAL STRUCTURE OF CU2+ BOUND H. PYROLI UREE RELATED ID: UREE_HELPY RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (2, 8)

Gene Ontology (9, 9)

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