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(-) Description

Title :  E. COLI NIFS/CSDB PROTEIN AT 2.0A WITH THE CYSTEINE PERSULFIDE INTERMEDIATE (RESIDUE CSS).
 
Authors :  C. D. Lima, S. K. Burley, New York Sgx Research Center For Structu Genomics (Nysgxrc)
Date :  16 Dec 01  (Deposition) - 21 Dec 01  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Persulfide Perselenide Nifs Pyridoxal Phosphate, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Lima
Analysis Of The E. Coli Nifs Csdb Protein At 2. 0 A Reveals The Structural Basis For Perselenide And Persulfide Intermediate Formation.
J. Mol. Biol. V. 315 1199 2002
PubMed-ID: 11827487  |  Reference-DOI: 10.1006/JMBI.2001.5308

(-) Compounds

Molecule 1 - SELENOCYSTEINE LYASE
    ChainsA
    EC Number4.4.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymNIFS/CSDB, SELENOCYSTEINE REDUCTASE, SELENOCYSTEINE BETA- LYASE, SCL

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:94 , THR A:95 , HIS A:123 , ALA A:125 , ASN A:175 , ASP A:200 , ALA A:202 , GLN A:203 , SER A:223 , HIS A:225 , LYS A:226 , GLY A:277 , THR A:278 , HOH A:596 , HOH A:623BINDING SITE FOR RESIDUE PLP A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SUFS_ECOLI217-236  1A:217-236
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SUFS_ECOLI217-236  2A:217-236

(-) Exons   (0, 0)

(no "Exon" information available for 1KMJ)

(-) 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:405
 aligned with SUFS_ECOLI | P77444 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
           SUFS_ECOLI     2 IFSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEGGGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNNIAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHCAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLLG 406
               SCOP domains d1kmja_ A: NifS-like protein/selenocysteine lyase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -1kmjA01 A:3-37,A:298-401           1kmjA02 A:38-297 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                1kmjA01 A:3-37,A:298-401 Aspartate Aminotransferase, domain 1                                           ----- CATH domains
               Pfam domains -----------------------Aminotran_5-1kmjA01 A:25-394                                                                                                                                                                                                                                                                                                                                                      ------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.ee..ee.ee.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..........hhhhhh..eeeee.hhh......eeeeehhhhhhhh.........eeeee...eeee...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeeee...hhhhhhhhhhhh.ee.eee...hhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kmj A   2 IFSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEGGGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNNIAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHcAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLLG 406
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361  |    371       381       391       401     
                                                                                                                                                                                                                                                                                                                                                                                                    364-CSS                                      

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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 Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (SUFS_ECOLI | P77444)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0031071    cysteine desulfurase activity    Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0009000    selenocysteine lyase activity    Catalysis of the reaction: L-selenocysteine + reduced acceptor = hydrogen selenide + L-alanine + acceptor.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006534    cysteine metabolic process    The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
    GO:0001887    selenium compound metabolic process    The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.
    GO:0006790    sulfur compound metabolic process    The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
    GO:0031162    sulfur incorporation into metallo-sulfur cluster    The incorporation of exogenous sulfur into a metallo-sulfur cluster.
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
        SUFS_ECOLI | P774441c0n 1i29 1jf9 1kmk 5db5

(-) Related Entries Specified in the PDB File

1jf9 NATIVE STRUCTURE
1kmj PERSELENIDE STRUCTURE RELATED ID: NYSGXRC-T129 RELATED DB: TARGETDB