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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 :  1.65
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 - BIOTIN SYNTHETASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Gene: TM_1269, THEMADRAFT_0043
    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  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
11N75Ligand/IonCHAPSO
2BR5Ligand/IonBROMIDE ION
3CO31Ligand/IonCARBONATE ION
4F3S1Ligand/IonFE3-S4 CLUSTER
5OTY1Mod. Amino Acid2-HYDROXY-L-TYROSINE
6SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
7SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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:529 , HOH A:567 , HOH A:801BINDING SITE FOR RESIDUE SAH A 402
03AC3SOFTWAREVAL A:97 , GLN A:98 , PHE A:99 , GLY A:100 , PRO A:276 , GLY A:277 , GLU A:280 , ARG A:284 , MET A:324 , LEU A:330 , 1N7 A:406 , 1N7 A:407 , HOH A:509 , HOH A:545 , HOH A:593 , HOH A:603 , HOH A:709 , HOH A:766 , HOH A:785 , HOH A:823BINDING 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 , 1N7 A:406 , HOH A:597 , HOH A:639 , HOH A:663 , HOH A:682 , HOH A:688 , HOH A:761BINDING SITE FOR RESIDUE 1N7 A 404
05AC5SOFTWAREARG A:29 , GLU A:33 , THR A:247 , LEU A:250 , 1N7 A:406 , HOH A:592 , HOH A:596 , HOH A:601 , HOH A:787 , HOH A:827BINDING SITE FOR RESIDUE 1N7 A 405
06AC6SOFTWARETHR A:317 , ALA A:318 , 1N7 A:403 , 1N7 A:404 , 1N7 A:405 , HOH A:712 , HOH A:824BINDING SITE FOR RESIDUE 1N7 A 406
07AC7SOFTWARELYS A:128 , PRO A:321 , MET A:324 , LYS A:325 , GLU A:328 , 1N7 A:403 , HOH A:724 , HOH A:772 , HOH A:777 , HOH A:785 , HOH A:803 , HOH A:837 , HOH A:847 , HOH A:849BINDING SITE FOR RESIDUE 1N7 A 407
08AC8SOFTWAREARG A:279 , CYS A:311 , CYS A:319 , CYS A:322 , HOH A:501BINDING SITE FOR RESIDUE F3S A 408
09AC9SOFTWAREARG A:54 , THR A:134 , ARG A:155BINDING SITE FOR RESIDUE BR A 409
10BC1SOFTWAREARG A:159 , ALA A:270 , TYR A:306 , HOH A:817 , HOH A:818BINDING SITE FOR RESIDUE BR A 410
11BC2SOFTWAREARG A:159 , PRO A:266 , HOH A:635BINDING SITE FOR RESIDUE BR A 411
12BC3SOFTWAREARG A:64 , HOH A:566 , HOH A:583BINDING SITE FOR RESIDUE BR A 412
13BC4SOFTWAREHOH A:872BINDING SITE FOR RESIDUE BR A 413
14BC5SOFTWAREPHE A:246 , HOH A:582 , HOH A:765BINDING SITE FOR RESIDUE CO3 A 414

(-) SS Bonds  (0, 0)

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

(-) 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 4JYE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JYE)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               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..eeeeeeee.....hhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jye A   1 MTGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYxMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKICVFEKDTACIPCVMKMIELLGRKPGRDWGGRKRVFET 347
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       
                                                                                                                                           114-OTY
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Met A:115 - Pro A:116   [ RasMol ]  
    Ser A:297 - Pro A:298   [ RasMol ]  
 

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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 4jy9 4jyd 4jyf 5fep 5fes 5few 5fex 5fez 5ff0 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

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