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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PROTEIN YHAK FROM ESCHERICHIA COLI
 
Authors :  D. Gurmu, J. Lu, K. A. Johnson, P. Nordlund, A. Holmgren, H. Erlandsen
Date :  18 Oct 07  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Ros, Bicupin, Sulfenic Acid, Reactive Cysteine, Cytosolic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Gurmu, J. Lu, K. A. Johnson, P. Nordlund, A. Holmgren, H. Erlandsen
The Crystal Structure Of The Protein Yhak From Escherichia Coli Reveals A New Subclass Of Redox Sensitive Enterobacterial Bicupins.
Proteins V. 74 18 2008
PubMed-ID: 18561187  |  Reference-DOI: 10.1002/PROT.22128

(-) Compounds

Molecule 1 - PIRIN-LIKE PROTEIN YHAK
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PT73.3
    Fragment: RESIDUES 2-233
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CYS122 IS OXIDIZED TO A SULFENIC ACID. AN INTRAMOLECULAR DISULFIDE BOND BETWEEN CYS10 AND CYS204.
    Synonym: YHAK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:37 , ALA A:38 , GLN A:157 , GLN A:158 , HOH A:2031BINDING SITE FOR RESIDUE CL A1234
2AC2SOFTWAREARG A:180 , LYS A:199 , ARG A:211BINDING SITE FOR RESIDUE CL A1235

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:10 -A:204

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:10 -Gly A:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VEC)

(-) 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    
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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:227
 aligned with YHAK_ECOLI | P42624 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:227
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       
           YHAK_ECOLI     7 ARQCGQADYGWLQARYTFSFGHYFDPKLLGYASLRVLNQEVLAPGAAFQPRTYPKVDILNVILDGEAEYRDSEGNHVQASAGEALLLSTQPGVSYSEHNLSKDKPLTRMQLWLDACPQRENPLIQKLALNMGKQQLIASPEGAMGSLQLRQQVWLHHIVLDKGESANFQLHGPRAYLQSIHGKFHALTHHEEKAALTCGDGAFIRDEANITLVADSPLRALLIDLPV 233
               SCOP domains d2veca_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Pirin-2vecA01 A:7-119                                                                                            ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh.eeee..............eeeeeeeee....eeeee....eeeeeeeee.eeeeee....eeeee..eeeee.......eeeee......eeeeeeeee.........eeeee.....eeeeee..hhhhhee.....eeeeeee....eeeee....eeeeeeee..eeeee..eeeeee....eeeee...eeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vec A   7 ARQCGQADYGWLQARYTFSFGHYFDPKLLGYASLRVLNQEVLAPGAAFQPRTYPKVDILNVILDGEAEYRDSEGNHVQASAGEALLLSTQPGVSYSEHNLSKDKPLTRMQLWLDAcPQRENPLIQKLALNMGKQQLIASPEGAMGSLQLRQQVWLHHIVLDKGESANFQLHGPRAYLQSIHGKFHALTHHEEKAALTCGDGAFIRDEANITLVADSPLRALLIDLPV 233
                                    16        26        36        46        56        66        76        86        96       106       116     | 126       136       146       156       166       176       186       196       206       216       226       
                                                                                                                                             122-CSO
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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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YHAK_ECOLI | P42624)
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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