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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPB FROM METHANOCALDOCOCCUS JANNASCHII IN THE TRIPHOSPHATE FORM, IN COMPLEX WITH ZINC
 
Authors :  R. Gasper, A. Scrima, A. Wittinghofer
Date :  23 Jun 06  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha And Beta Protein, P-Loop Containing Nucleoside Triphosphate Hydrolase, Hydrolase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Gasper, A. Scrima, A. Wittinghofer
Structural Insights Into Hypb, A Gtp-Binding Protein That Regulates Metal Binding.
J. Biol. Chem. V. 281 27492 2006
PubMed-ID: 16807243  |  Reference-DOI: 10.1074/JBC.M600809200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE HYDROGENASE NICKEL INCORPORATION PROTEIN HYPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T3
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HYPB
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1GSP2Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:47 , ASP A:75 , GLU A:120 , GSP A:300 , HOH A:468BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWARETHR B:47 , ASP B:75 , GLU B:120 , GSP B:300 , HOH B:437BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWARECYS A:95 , CYS A:127 , CYS B:95 , ZN B:402BINDING SITE FOR RESIDUE ZN A 401
4AC4SOFTWAREZN A:401 , CYS B:95 , HIS B:96 , CYS B:127 , HOH B:462BINDING SITE FOR RESIDUE ZN B 402
5AC5SOFTWAREHIS A:100 , HIS A:104 , HIS B:100 , HIS B:104BINDING SITE FOR RESIDUE ZN A 403
6AC6SOFTWAREHIS A:100 , HIS A:104 , HIS B:100 , HIS B:104BINDING SITE FOR RESIDUE ZN B 404
7AC7SOFTWAREGLY A:43 , SER A:44 , GLY A:45 , LYS A:46 , THR A:47 , LEU A:48 , ASP A:75 , ARG A:78 , GLU A:120 , ASN A:167 , LYS A:168 , ASP A:170 , SER A:199 , LEU A:200 , LYS A:201 , MG A:301 , HOH A:416 , HOH A:458 , HOH A:464 , HOH A:465 , HOH A:468 , GLU B:146 , LYS B:153 , ALA B:174 , VAL B:175BINDING SITE FOR RESIDUE GSP A 300
8AC8SOFTWAREGLU A:146 , LYS A:153 , ALA A:174 , VAL A:175 , ILE B:42 , GLY B:43 , SER B:44 , GLY B:45 , LYS B:46 , THR B:47 , LEU B:48 , ASP B:75 , ARG B:78 , GLU B:120 , ASN B:167 , LYS B:168 , ASP B:170 , LEU B:171 , SER B:199 , LEU B:200 , LYS B:201 , MG B:301 , HOH B:422 , HOH B:437 , HOH B:453 , HOH B:463BINDING SITE FOR RESIDUE GSP B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HF8)

(-) Exons   (0, 0)

(no "Exon" information available for 2HF8)

(-) 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:211
 aligned with HYPB_METJA | Q57884 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:211
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           HYPB_METJA    11 KDILKANKRLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLKDKYKIACIAGDVIAKFDAERMEKHGAKVVPLNTGKECHLDAHLVGHALEDLNLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGIMKTADLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLSLKTMEGFDKVLEFIEKSVKEVK 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.eeeee.....hhhhhh.....eeeeeee.hhh.hhhhhhhhhhh...eeeeehhhhhhhhh.hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hf8 A  11 KDILKANKRLADKNRKLLNKHGVVAFDFmGAIGSGKTLLIEKLIDNLKDKYKIACIAGDVIAKFDAERmEKHGAKVVPLNTGKECHLDAHLVGHALEDLNLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGImKTADLIVINKIDLADAVGADIKKmENDAKRINPDAEVVLLSLKTmEGFDKVLEFIEKSVKEVK 221
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 |     190       200  |    210       220 
                                                       39-MSE                                  79-MSE                                                                        158-MSE                 182-MSE              203-MSE              


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with HYPB_METJA | Q57884 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:209
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           HYPB_METJA    12 DILKANKRLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLKDKYKIACIAGDVIAKFDAERMEKHGAKVVPLNTGKECHLDAHLVGHALEDLNLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGIMKTADLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLSLKTMEGFDKVLEFIEKSVKEV 220
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.eeeee.....hhhhhh.....eeeeeee.hhh......hhhhhhhh.eeeeehhhhhhhhh.hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hf8 B  12 DILKANKRLADKNRKLLNKHGVVAFDFmGAIGSGKTLLIEKLIDNLKDKYKIACIAGDVIAKFDAERmEKHGAKVVPLNTGKECHLDAHLVGHALEDLNLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGImKTADLIVINKIDLADAVGADIKKmENDAKRINPDAEVVLLSLKTmEGFDKVLEFIEKSVKEV 220
                                    21        31       |41        51        61        71       |81        91       101       111       121       131       141       151      |161       171       181|      191       201 |     211         
                                                      39-MSE                                  79-MSE                                                                        158-MSE                 182-MSE              203-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2HF8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HF8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HYPB_METJA | Q57884)
molecular function
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
biological process
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0051604    protein maturation    Any process leading to the attainment of the full functional capacity of a protein.

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  2hf8
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 Related Entries

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        HYPB_METJA | Q57884: 2hf9

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