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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 :  28 Mar 13  (Deposition) - 01 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
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 Plasmid: PHYDE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PT7-7
    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  (10, 16)

Asymmetric/Biological Unit (10, 16)
No.NameCountTypeFull Name
11N75Ligand/IonCHAPSO
2CL2Ligand/IonCHLORIDE ION
3CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
4FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5GOL1Ligand/IonGLYCEROL
6H2S2Ligand/IonHYDROSULFURIC ACID
7IPA1Ligand/IonISOPROPYL ALCOHOL
8SAM1Ligand/IonS-ADENOSYLMETHIONINE
9SF41Ligand/IonIRON/SULFUR CLUSTER
10SO41Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:67 , CYS A:70 , GLY A:109 , SAM A:402BINDING SITE FOR RESIDUE SF4 A 401
02AC2SOFTWARETYR A:69 , SER A:108 , SER A:136 , GLY A:138 , ARG A:159 , GLU A:161 , ARG A:180 , MET A:199 , PRO A:229 , ILE A:231 , TYR A:303 , LEU A:305 , TYR A:306 , SF4 A:401 , HOH A:511 , HOH A:517 , HOH A:519 , HOH A:528 , HOH A:567BINDING SITE FOR RESIDUE SAM 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 , IPA A:412 , HOH A:508 , HOH A:544 , HOH A:594 , HOH A:606 , HOH A:812 , HOH A:813BINDING 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:648 , HOH A:676 , HOH A:695 , HOH A:701 , HOH A:821BINDING SITE FOR RESIDUE 1N7 A 404
05AC5SOFTWAREARG A:29 , GLU A:33 , THR A:247 , LEU A:250 , 1N7 A:406 , HOH A:593 , HOH A:597 , HOH A:603 , HOH A:798BINDING SITE FOR RESIDUE 1N7 A 405
06AC6SOFTWAREARG A:29 , LYS A:315 , THR A:317 , ALA A:318 , 1N7 A:403 , 1N7 A:405 , 1N7 A:407 , HOH A:632 , HOH A:728 , HOH A:828BINDING SITE FOR RESIDUE 1N7 A 406
07AC7SOFTWARELYS A:128 , PRO A:321 , MET A:324 , LYS A:325 , GLU A:328 , 1N7 A:403 , 1N7 A:406 , HOH A:530 , HOH A:744 , HOH A:799 , HOH A:805BINDING SITE FOR RESIDUE 1N7 A 407
08AC8SOFTWAREVAL A:47 , HIS A:52 , ASP A:262 , ASN A:264 , GLY A:340 , ARG A:341 , LYS A:342 , HOH A:550BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREARG A:279 , CYS A:311 , CYS A:319 , CYS A:322 , VAL A:323 , H2S A:410 , H2S A:411 , HOH A:622BINDING SITE FOR RESIDUE FES A 409
10BC1SOFTWARECYS A:311 , CYS A:319 , FES A:409BINDING SITE FOR RESIDUE H2S A 410
11BC2SOFTWAREARG A:279 , CYS A:322 , MET A:326 , FES A:409BINDING SITE FOR RESIDUE H2S A 411
12BC3SOFTWARELYS A:102 , LYS A:325 , 1N7 A:403 , HOH A:570 , HOH A:779BINDING SITE FOR RESIDUE IPA A 412
13BC4SOFTWAREARG A:54 , THR A:134 , ARG A:155 , MET A:224BINDING SITE FOR RESIDUE CL A 413
14BC5SOFTWAREARG A:159 , THR A:269 , ALA A:270 , TYR A:306 , HOH A:822BINDING SITE FOR RESIDUE CL A 414
15BC6SOFTWAREASP A:337 , TRP A:338 , GLY A:339 , GLY A:340 , LYS A:342 , HOH A:536 , HOH A:720BINDING SITE FOR RESIDUE SO4 A 415

(-) SS Bonds  (0, 0)

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

(-) 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 4JXC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JXC)

(-) 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.....eehhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jxc 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      
                                                                                                                                                                                                               183-CSO
   Legend:   → Mismatch (orange background)
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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 4JXC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4jy8 4jy9 4jyd 4jye 4jyf 5fep 5fes 5few 5fex 5fez 5ff0 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

3ciw INTERMEDIATE STATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION
3iix INTERMEDIATE STATES IN THE TIME COURSE OF FES CLUSTER DEGRADATION
4jy8
4jy9
4jye
4jyf