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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO NI2+
 
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 :  1.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metal Binding 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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1FMT10Ligand/IonFORMIC ACID
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:102 , GLU B:4 , HIS B:102 , HIS B:152 , HOH B:249BINDING SITE FOR RESIDUE NI B 171
02AC2SOFTWAREASN A:74 , LEU A:76 , ASP A:77 , SER A:137 , HOH A:217 , HOH A:237BINDING SITE FOR RESIDUE FMT A 171
03AC3SOFTWAREARG A:31 , ARG A:145 , HOH A:194 , ILE B:34 , ARG B:36BINDING SITE FOR RESIDUE FMT B 172
04AC4SOFTWAREHIS B:82 , GLN B:132 , ARG B:134BINDING SITE FOR RESIDUE FMT B 173
05AC5SOFTWAREILE A:34 , ARG B:31 , ARG B:145 , HOH B:182BINDING SITE FOR RESIDUE FMT B 174
06AC6SOFTWAREARG A:48 , ARG B:101 , GLU B:119BINDING SITE FOR RESIDUE FMT B 175
07AC7SOFTWAREHIS A:82 , GLN A:132 , ARG A:134BINDING SITE FOR RESIDUE FMT A 172
08AC8SOFTWAREARG A:40 , ASN A:74 , HOH A:217 , HOH A:237BINDING SITE FOR RESIDUE FMT A 173
09AC9SOFTWAREGLN A:84 , SER A:110 , PHE A:112 , GLN B:84 , SER B:110 , PHE B:112 , HOH B:222BINDING SITE FOR RESIDUE FMT B 176
10BC1SOFTWAREARG B:40 , ASN B:74BINDING SITE FOR RESIDUE FMT B 177
11BC2SOFTWAREGLN A:111 , HOH A:183 , HOH A:221 , HOH A:248 , ALA B:89BINDING SITE FOR RESIDUE FMT A 174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3TJ8)

(-) Sequences/Alignments

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:149
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....ee.hhhhhhhheeeeeeehhhhh...eeeee.....eeeee............eeeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh...eee.....eeeee.hhhhhhhhhhhh.eeeeeee..hhh.ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj8 A   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVS 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPH 152
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhheeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj8 B   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPH 152
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TJ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TJ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TJ8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UREE_HELPY | Q09064: 3l9z 3la0 3nxz 3ny0 3tj9 3tja

(-) Related Entries Specified in the PDB File

3tj9 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO ZN2+
3tja CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE IN THE APO FORM