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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE HOLLIDAY JUNCTION RESOLVASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE HOLLIDAY JUNCTION RESOLVASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YRRK, BSU27390
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VHX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VHX)

(-) Exons   (0, 0)

(no "Exon" information available for 1VHX)

(-) 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:140
 aligned with YQGF_BACSU | O34634 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:140
                             1                                                                                                                                      138 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129        |-
           YQGF_BACSU     - -MRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLDSLN-   -
               SCOP domains d1vhxa_ A: Hypothetical protein YrrK (RuvX)                                                                                                  SCOP domains
               CATH domains 1vhxA00 A:0-139 Ribonuclease H-like (UPF0081)                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeee......eeeeeeee.hhhhh..hhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhx A   0 SLRILGLDLGTKTLGVALSDEmGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNmNGTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTmAAEKmLIAADVSRQKRKKVIDKmAAVmILQGYLDSLNE 139
                                     9        19 |      29        39        49        59     |  69        79        89        99 |    |109       119    |  129       139
                                                21-MSE                                      65-MSE                             101-MSE|               124-MSE           
                                                                                                                                    106-MSE               128-MSE       


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with YQGF_BACSU | O34634 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:138
                             1                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129        
           YQGF_BACSU     - -MRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLDSL 137
               SCOP domains d1vhxb_ B: Hypothetical protein YrrK (RuvX)                                                                                                SCOP domains
               CATH domains 1vhxB00 B:0-137 Ribonuclease H-like (UPF0081)                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee......eeeeeeee.hhhhh..hhhhhhhhh....eeeeeee.........hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhx B   0 SLRILGLDLGTKTLGVALSDEmGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNmNGTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTmAAEKmLIAADVSRQKRKKVIDKmAAVmILQGYLDSL 137
                                     9        19 |      29        39        49        59     |  69        79        89        99 |    |109       119    |  129        
                                                21-MSE                                      65-MSE                             101-MSE|               124-MSE         
                                                                                                                                    106-MSE               128-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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VHX)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YQGF_BACSU | O34634)
molecular function
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0000967    rRNA 5'-end processing    Any process involved in forming the mature 5' end of an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    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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  1vhx
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 Related Entries

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

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