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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTEINYL-TRNA(PRO) DEACYLASE FROM H. INFLUENZAE (HI1434)
 
Authors :  H. Zhang, K. Huang, Z. Li, O. Herzberg, Structure 2 Function Project (S2F)
Date :  03 Nov 99  (Deposition) - 14 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Ybak, Structure 2 Function Project, S2F, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhang, K. Huang, Z. Li, L. Banerjei, K. E. Fisher, N. V. Grishin, E. Eisenstein, O. Herzberg
Crystal Structure Of Ybak Protein From Haemophilus Influenzae (Hi1434) At 1. 8 A Resolution: Functional Implications.
Proteins V. 40 86 2000 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINYL-TRNA(PRO) DEACYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: YCYB2
    Gene: YBAK
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Other Details: IMPACT I SYSTEM FROM NEW ENGLAND BIOLABS
    Synonym: HI1434

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1DBX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DBX)

(-) 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:152
 aligned with YBAK_HAEIN | P45202 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           YBAK_HAEIN     2 TPAIDLLKKQKIPFILHTYDHDPNNQHFGDEAAEKLGIDPNRSFKTLLVAENGDQKKLACFVLATANMLNLKKAAKSIGVKKVEMADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFETIYVSGGKRGLSVEIAPQDLAKVLGAEFTDIVDE 158
               SCOP domains d1dbxa_ A: Hypothetical      protein HI1434 (YbaK homologue)                                                                                                  SCOP domains
               CATH domains 1dbxA00 A:2-158  [code=     3.90.960.10, no name defined]                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeee.....-----.hhhhhhhh.hhhh.eeeeeeee......eeeeeee.....hhhhhhhhh....eee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dbx A   2 TPAIDLLKKQKIPFILHTYDHDP-----GDEAAEKLGIDPNRSFKTLLVAENGDQKKLACFVLATANmLNLKKAAKSIGVKKVEmADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFETIYVSGGKRGLSVEIAPQDLAKVLGAEFTDIVDE 158
                                    11        21  |     31        41        51        61       |71        81    |   91       101       111       121       131       141       151       
                                                 24    30                                     69-MSE           86-MSE                                                                    


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with YBAK_HAEIN | P45202 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           YBAK_HAEIN     2 TPAIDLLKKQKIPFILHTYDHDPNNQHFGDEAAEKLGIDPNRSFKTLLVAENGDQKKLACFVLATANMLNLKKAAKSIGVKKVEMADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFETIYVSGGKRGLSVEIAPQDLAKVLGAEFTDIVDE 158
               SCOP domains d1dbxb_ B: Hypothetical      protein HI1434 (YbaK homologue)                                                                                                  SCOP domains
               CATH domains 1dbxB00 B:2-158  [code=     3.90.960.10, no name defined]                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeee.....-----.hhhhhhhh.hhh.eeeeeeeee..eeeeeeeeeee.....hhhhhhhhh....eee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dbx B   2 TPAIDLLKKQKIPFILHTYDHDP-----GDEAAEKLGIDPNRSFKTLLVAENGDQKKLACFVLATANmLNLKKAAKSIGVKKVEmADKDAAQKSTGYLVGGISPLGQKKRVKTVINSTALEFETIYVSGGKRGLSVEIAPQDLAKVLGAEFTDIVDE 158
                                    11        21  |     31        41        51        61       |71        81    |   91       101       111       121       131       141       151       
                                                 24    30                                     69-MSE           86-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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YBAK_HAEIN | P45202)
molecular function
    GO:0043906    Ala-tRNA(Pro) hydrolase activity    Catalysis of the hydrolysis of misacylated Ala-tRNA(Pro).
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
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
        YBAK_HAEIN | P45202: 1dbu

(-) Related Entries Specified in the PDB File

1dbu RELATED ID: HI1434 RELATED DB: TARGETDB