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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE IN THE APO FORM
 
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 :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:1 , ILE D:3 , GLU D:4 , ARG D:5BINDING SITE FOR RESIDUE SO4 D 171
2AC2SOFTWAREARG C:31 , LYS C:33 , ILE C:34BINDING SITE FOR RESIDUE SO4 C 171
3AC3SOFTWAREARG A:31 , LYS A:32 , LYS A:33 , HOH A:193BINDING SITE FOR RESIDUE SO4 A 171
4AC4SOFTWAREILE B:3 , GLU B:4 , ARG B:5 , MET D:1BINDING SITE FOR RESIDUE SO4 B 171
5AC5SOFTWAREASN A:74 , ASP A:77 , LYS A:139 , ASN C:74 , ASP C:77 , LYS C:139BINDING SITE FOR RESIDUE CL A 172

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TJA)

(-) Sequences/Alignments

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: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 ........hhhhhhhhhheeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhhh.eeeeeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tja 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:150
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSM 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhheeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhhh.eeeeeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tja B   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSM 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


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

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.....eeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhh....ee.....eeeee.hhhhhhhhhhh..eeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tja C   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTV 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain D from PDB  Type:PROTEIN  Length:150
 aligned with UREE_HELPY | Q09064 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           UREE_HELPY     1 MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSM 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhheeeeeeehhhhh...eeeee.....eeeee.............eeeee..eeeeeee..eeeeeee..hhhhhhhhhhhhhhhh...ee.....eeeee.hhhhhhhhhhhh.eeeeeee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tja D   1 MIIERLVGNLRDLNPLDFSVDYVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSM 150
                                    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 3TJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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.

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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 3tj8 3tj9

(-) Related Entries Specified in the PDB File

3tj8 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO NI2+
3tj9 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREE BOUND TO ZN2+