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(-) Description

Title :  STRUCTURE OF B. SUBTILIS YLQF GTPASE
 
Authors :  R. Kniewel, J. Buglino, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  24 Jun 03  (Deposition) - 08 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Nysgxrc T18, Gtpase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kniewel, J. Buglino, C. D. Lima
Structure Of The Ylqf Gtpase From B. Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN YLQF
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Strain: B834 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YLQF
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: YLQF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:134 , GNP A:501 , HOH A:9036 , HOH A:9108 , HOH A:9150BINDING SITE FOR RESIDUE MG A 9001
2AC2SOFTWARELYS A:49 , ASN A:58 , LYS A:59 , ASP A:61 , LYS A:62 , ASN A:86 , SER A:87 , VAL A:88 , PRO A:129 , ASN A:130 , VAL A:131 , GLY A:132 , LYS A:133 , SER A:134 , THR A:135 , GLY A:174 , MG A:9001 , HOH A:9036 , HOH A:9037 , HOH A:9108 , HOH A:9141 , HOH A:9146 , HOH A:9163BINDING SITE FOR RESIDUE GNP A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PUJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PUJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PUJ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_CPPS51721 Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.RBGA_BACSU14-178  1A:14-178

(-) Exons   (0, 0)

(no "Exon" information available for 1PUJ)

(-) 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:261
 aligned with RBGA_BACSU | O31743 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:273
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
           RBGA_BACSU     9 HMAKARREVTEKLKLIDIVYELVDARIPMSSRNPMIEDILKNKPRIMLLNKADKADAAVTQQWKEHFENQGIRSLSINSVNGQGLNQIVPASKEILQEKFDRMRAKGVKPRAIRALIIGIPNVGKSTLINRLAKKNIAKTGDRPGITTSQQWVKVGKELELLDTPGILWPKFEDELVGLRLAVTGAIKDSIINLQDVAVFGLRFLEEHYPERLKERYGLDEIPEDIAELFDAIGEKRGCLMSGGLINYDKTTEVIIRDIRTEKFGRLSFEQPT 281
               SCOP domains d1puja_ A: Probable GTPase YlqF                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---1pujA01 A:12-179 P-loop containing nucleotide triphosphate hydrolases                                                                                                   1pujA02 A:180-272  [code=1.10.1580.10, no name defined]                                      --------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------MMR_HSR1-1pujA01 A:122-24            5                                                                                      ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeee........hhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhh....------------..eee...eeeee..........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----G_CP  PDB: A:14-178 UniProt: 14-178                                                                                                                                  ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1puj A   9 HMAKARREVTEKLKLIDIVYELVDARIPMSSRNPMIEDILKNKPRIMLLNKADKADAAVTQQWKEHFENQGIRSLSINSVNGQGLNQIVPASKEILQEKFDRMRAKGVKPRAIRALIIGIPNVGKSTLINRLAKKNIA------------QWVKVGKELELLDTPGILWPKFEDELVGLRLAVTGAIKDSIINLQDVAVFGLRFLEEHYPERLKERYGLDEIPEDIAELFDAIGEKRGCLMSGGLINYDKTTEVIIRDIRTEKFGRLSFEQPT 281
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       | -         -|      168       178       188       198       208       218       228       238       248       258       268       278   
                                                                                                                                                                   146          159
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RBGA_BACSU | O31743)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
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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