3TJ9 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO ZN2+

Authors :   K. Banaszak, M. Bellucci, B. Zambelli, W. R. Rypniewski, S. Ciurli

Date :   24 Aug 11 (Deposition) - 02 Nov 11 (Release) - 01 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.52

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

Keywords :   Metal Binding Protein, Urease Accessory Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Banaszak, V. Martin-Diaconescu, M. Bellucci, B. Zambelli, W. Rypniewski, M. J. Maroney, S. Ciurli
Crystallographic And X-Ray Absorption Spectroscopic Characterization Of Helicobacter Pylori Uree Bound To Ni2+ And Zn2+ Reveals A Role For The Disordered C-Terminal Arm I Metal Trafficking.
Biochem. J. V. 441 1017 2012
PubMed-ID: 22010876 | Reference-DOI: 10.1042/BJ20111659

Molecule 1 - UREASE ACCESSORY PROTEIN UREE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UREE, HP_0070
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:102 , GLU A:154 , HIS B:102 , HIS B:152 , HIS D:152	BINDING SITE FOR RESIDUE ZN A 171
2	AC2	SOFTWARE	GLU A:127 , ASN A:133	BINDING SITE FOR RESIDUE FMT A 172
3	AC3	SOFTWARE	HIS A:152 , HIS C:102 , HIS C:152 , HIS D:102 , GLU D:154	BINDING SITE FOR RESIDUE ZN C 171

(no "SS Bond" information available for 3TJ9)

Asymmetric Unit

No.	Residues
1	His C:152	-	Ser C:153

(no "SAP(SNP)/Variant" information available for 3TJ9)

(no "PROSITE Motif" information available for 3TJ9)

(no "Exon" information available for 3TJ9)

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:155
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSEP 155
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhheeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh...eee.....eeeee.hhhhhhhhhhh..eeeeeee..hhh.ee.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj9 A   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSEP 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHS 153
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.hhhhhhhheeeeeeehhhhh...eeeee.....eeeee............eeeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhhh.eeeeeee..hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj9 B   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHS 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eee.hhhhhhhheeeeeeehhhhh...eeeee.....eeeee............eeeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj9 C   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh........eeeehhhhh...eeeee.....eeeee.............eee......eeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj9 D   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSE 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 3TJ9)

(no "CATH Domain" information available for 3TJ9)

(no "Pfam Domain" information available for 3TJ9)

Asymmetric 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 Unit
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His C:152 - Ser C:153	[ RasMol ]

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

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	3tj9
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	UREE_HELPY \| Q09064
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	UREE_HELPY \| Q09064	:	3l9z 3la0 3nxz 3ny0 3tj8 3tja

3tj8	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO NI2+
3tja	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE IN THE APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (9, 9)

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