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(-) Description

Title :  X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TIME COURSE OF SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS
 
Authors :  Y. Nicolet, R. Rohac, L. Martin, J. C. Fontecilla-Camps
Date :  29 Mar 13  (Deposition) - 01 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Radical Sam Protein, Fefe-Hydrogenase Active Site Assembly, Fe4S4 Cluster, S-Adenosyl-L-Methionine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nicolet, R. Rohac, L. Martin, J. C. Fontecilla-Camps
X-Ray Snapshots Of Possible Intermediates In The Time Cours Of Synthesis And Degradation Of Protein-Bound Fe4S4 Clusters.
Proc. Natl. Acad. Sci. Usa V. 110 7188 2013
PubMed-ID: 23596207  |  Reference-DOI: 10.1073/PNAS.1302388110

(-) Compounds

Molecule 1 - FEFE-HYDROGENASE MATURASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: THEMADRAFT_0043, TM1269, TM_1269
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: RADICAL SAM DOMAIN PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
11N77Ligand/IonCHAPSO
2CL3Ligand/IonCHLORIDE ION
3FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:67 , CYS A:70 , SAH A:402BINDING SITE FOR RESIDUE SF4 A 401
02AC2SOFTWARETYR A:69 , SER A:108 , SER A:136 , ARG A:159 , GLU A:161 , ARG A:180 , MET A:199 , PRO A:229 , ILE A:231 , TYR A:303 , LEU A:305 , SF4 A:401 , HOH A:512 , HOH A:518 , HOH A:520 , HOH A:567 , HOH A:652 , HOH A:829BINDING SITE FOR RESIDUE SAH A 402
03AC3SOFTWAREGLN A:98 , PHE A:99 , GLY A:100 , GLU A:280 , ARG A:284 , MET A:324 , LEU A:330 , 1N7 A:406 , 1N7 A:407 , 1N7 A:410 , HOH A:509 , HOH A:544 , HOH A:594 , HOH A:606 , HOH A:828BINDING SITE FOR RESIDUE 1N7 A 403
04AC4SOFTWARELYS A:37 , ASP A:40 , LYS A:170 , ARG A:284 , SER A:297 , LYS A:315 , ASP A:316 , THR A:317 , HOH A:598 , HOH A:647 , HOH A:675 , HOH A:693 , HOH A:699BINDING SITE FOR RESIDUE 1N7 A 404
05AC5SOFTWAREARG A:29 , GLU A:33 , THR A:247 , 1N7 A:406 , HOH A:593 , HOH A:597 , HOH A:603 , HOH A:797BINDING SITE FOR RESIDUE 1N7 A 405
06AC6SOFTWAREARG A:29 , LYS A:315 , THR A:317 , ALA A:318 , 1N7 A:403 , 1N7 A:405 , HOH A:725 , HOH A:728 , HOH A:790 , HOH A:826BINDING SITE FOR RESIDUE 1N7 A 406
07AC7SOFTWARELYS A:128 , MET A:324 , LYS A:325 , GLU A:328 , 1N7 A:403 , HOH A:707 , HOH A:742 , HOH A:779 , HOH A:780BINDING SITE FOR RESIDUE 1N7 A 407
08AC8SOFTWAREASP A:337 , TRP A:338 , GLY A:339 , GLY A:340 , LYS A:342BINDING SITE FOR RESIDUE 1N7 A 408
09AC9SOFTWAREARG A:279 , CYS A:311 , CYS A:319 , CYS A:322 , HOH A:501BINDING SITE FOR RESIDUE FES A 409
10BC1SOFTWAREGLY A:100 , LYS A:102 , LYS A:325 , 1N7 A:403 , HOH A:570 , HOH A:776BINDING SITE FOR RESIDUE 1N7 A 410
11BC2SOFTWAREARG A:54 , THR A:134 , ARG A:155BINDING SITE FOR RESIDUE CL A 411
12BC3SOFTWAREARG A:159 , MET A:291 , HOH A:643 , HOH A:845BINDING SITE FOR RESIDUE CL A 412
13BC4SOFTWAREARG A:159 , THR A:268 , THR A:269 , ALA A:270 , TYR A:306 , HOH A:829 , HOH A:842 , HOH A:843BINDING SITE FOR RESIDUE CL A 413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JY9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:115 -Pro A:116
2Ser A:297 -Pro A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JY9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JY9)

(-) Exons   (0, 0)

(no "Exon" information available for 4JY9)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee........................hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eee......hhhhhhhhh...hhhhhhhhhhhhhhh..eeee..ee.....hhhhhhhhhhhhhhhh..ee..ee...............hhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jy9 A   2 TGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYYMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKICVFEKDTACIPCVMKMIELLGRKPGRDWGGRKRVFET 347
                                    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
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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  (0, 0)

(no "SCOP Domain" information available for 4JY9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JY9)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        HYDE_THEMA | Q9X0Z6: 3ciw 3cix 3iix 3iiz 4jxc 4jy8 4jyd 4jye 4jyf 5fep 5fes 5few 5fex 5fez 5ff0 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

3ciw INTERMEDIATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION UPON OXYGEN EXPOSURE
3iix INTERMEDIATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION UPON OXYGEN EXPOSURE
4jxc INTERMEDIATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION UPON OXYGEN EXPOSURE
4jy8 INTERMEDIATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION UPON OXYGEN EXPOSURE
4jy9
4jye
4jyf