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(-) Description

Title :  X-RAY STRUCTURE OF THE FEFE-HYDROGENASE MATURASE HYDE FROM T. MARITIMA IN COMPLEX WITH S-ADENOSYL-L-METHIONINE
 
Authors :  Y. Nicolet, P. Amara, J. M. Mouesca, J. C. Fontecilla-Camps
Date :  03 Aug 09  (Deposition) - 22 Sep 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A
Keywords :  Adomet Radical, Sam Radical, Hyde, Hydrogenase, Fe4S4 Cluster, Adomet Cleavage, Maturation, Adenosylmethionine, Adomet Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nicolet, P. Amara, J. -M. Mouesca, J. C. Fontecilla-Camps
Unexpected Electron Transfer Mechanism Upon Adomet Cleavage In Radical Sam Proteins
Proc. Natl. Acad. Sci. Usa 2009
PubMed-ID: 19706452  |  Reference-DOI: 10.1073/PNAS.0904385106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIOTIN SYNTHETASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Gene: TM_1269
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Strain: MSB8
    Synonym: FEFE-HYDROGENASE MATURASE HYDE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 15)

Asymmetric/Biological Unit (9, 15)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CO31Ligand/IonCARBONATE ION
3CPS5Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
4CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
5FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
6H2S2Ligand/IonHYDROSULFURIC ACID
7OTY1Mod. Amino Acid2-AMINO-3-(4-HYDROXY-6-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC ACID
8SAM1Ligand/IonS-ADENOSYLMETHIONINE
9SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:63 , CYS A:67 , CYS A:70 , SAM A:1501BINDING SITE FOR RESIDUE SF4 A 2460
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 , HOH A:458 , HOH A:464 , HOH A:466 , HOH A:475 , HOH A:514 , HOH A:780 , SF4 A:2460BINDING SITE FOR RESIDUE SAM A 1501
03AC3SOFTWAREGLN A:98 , PHE A:99 , GLY A:100 , LYS A:102 , GLU A:280 , ARG A:284 , MET A:324 , LYS A:325 , LEU A:329 , LEU A:330 , HOH A:455 , HOH A:491 , HOH A:517 , HOH A:541 , HOH A:553 , HOH A:672 , HOH A:754 , HOH A:777 , CPS A:1703 , CPS A:1704 , CPS A:1705BINDING SITE FOR RESIDUE CPS A 1701
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:353 , HOH A:382 , HOH A:414 , HOH A:545 , HOH A:595 , HOH A:623 , HOH A:648 , HOH A:762BINDING SITE FOR RESIDUE CPS A 1702
05AC5SOFTWAREARG A:29 , GLU A:33 , THR A:247 , LEU A:250 , HOH A:540 , HOH A:544 , HOH A:550 , HOH A:739 , HOH A:782 , CPS A:1701 , CPS A:1704BINDING SITE FOR RESIDUE CPS A 1703
06AC6SOFTWAREARG A:29 , LYS A:315 , THR A:317 , ALA A:318 , HOH A:376 , HOH A:406 , HOH A:418 , HOH A:440 , HOH A:579 , HOH A:675 , CPS A:1701 , CPS A:1703BINDING SITE FOR RESIDUE CPS A 1704
07AC7SOFTWARELYS A:128 , MET A:324 , LYS A:325 , GLU A:328 , HOH A:656 , HOH A:690 , HOH A:723 , HOH A:724 , CPS A:1701BINDING SITE FOR RESIDUE CPS A 1705
08AC8SOFTWAREARG A:279 , CYS A:311 , CYS A:319 , CYS A:322 , VAL A:323 , HOH A:569 , H2S A:2649 , H2S A:2650BINDING SITE FOR RESIDUE FES A 2648
09AC9SOFTWARECYS A:311 , CYS A:319 , FES A:2648BINDING SITE FOR RESIDUE H2S A 2649
10BC1SOFTWAREARG A:279 , CYS A:322 , MET A:326 , FES A:2648BINDING SITE FOR RESIDUE H2S A 2650
11BC2SOFTWAREARG A:54 , THR A:134 , ARG A:155BINDING SITE FOR RESIDUE CL A 349
12BC3SOFTWAREARG A:159 , THR A:269 , ALA A:270 , TYR A:306 , HOH A:435 , HOH A:710BINDING SITE FOR RESIDUE CL A 350
13BC4SOFTWAREPHE A:246 , HOH A:499 , HOH A:530BINDING SITE FOR RESIDUE CO3 A 351

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IIZ)

(-) 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 3IIZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IIZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3IIZ)

(-) 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
 aligned with HYDE_THEMA | Q9X0Z6 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    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      
           HYDE_THEMA     2 TGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYYMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKICVFEKDTACIPCVMKMIELLGRKPGRDWGGRKRVFET 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..eeee..ee.....hhhhhhhhhhhhhhhh..ee..ee...............hhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh....ee........hhhhh..............hhhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iiz 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      
                                                                                                                                          114-OTY                                                              183-CSO
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3IIZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IIZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IIZ)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HYDE_THEMA | Q9X0Z6)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HYDE_THEMA | Q9X0Z6: 3ciw 3cix 3iix 4jxc 4jy8 4jy9 4jyd 4jye 4jyf 5fep 5fes 5few 5fex 5fez 5ff0 5ff2 5ff3 5ff4

(-) Related Entries Specified in the PDB File

3ciw 3cix 3iix