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(-) Description

Title :  STRUCTURE OF THE COVALENT ACYL-ADENYLATE FORM OF THE MOEB-MOAD PROTEIN COMPLEX
 
Authors :  M. W. Lake, M. M. Wuebbens, K. V. Rajagopalan, H. Schindelin
Date :  03 Sep 01  (Deposition) - 21 Nov 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  B,D
Biol. Unit 1:  B,D  (2x)
Keywords :  Moeb: Modified Rossmann Fold; (2) Cys-X-X-Cys Zinc-Binding Motifs; Moad: Ubiquitin-Like Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Lake, M. M. Wuebbens, K. V. Rajagopalan, H. Schindelin
Mechanism Of Ubiquitin Activation Revealed By The Structure Of A Bacterial Moeb-Moad Complex.
Nature V. 414 325 2001
PubMed-ID: 11713534  |  Reference-DOI: 10.1038/35104586

(-) Compounds

Molecule 1 - MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneMOEB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneMOAD
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymMOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit BD
Biological Unit 1 (2x)BD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:172 , CYS B:175 , CYS B:244 , CYS B:247BINDING SITE FOR RESIDUE ZN B 250
2AC2SOFTWAREARG B:14 , SER B:69 , ASN B:70 , ARG B:73 , HOH D:84BINDING SITE FOR RESIDUE SO4 B 251
3AC3SOFTWAREGLY B:38 , GLY B:40 , GLY B:41 , LEU B:61 , ASP B:62 , PHE B:63 , ASP B:64 , ARG B:73 , GLN B:74 , LYS B:86 , LEU B:109 , CYS B:128 , THR B:129 , ASP B:130 , ASN B:131 , VAL B:134 , HOH B:266 , HOH B:281 , HOH B:310 , GLY D:81 , HOH D:84 , HOH D:90 , HOH D:102 , HOH D:105BINDING SITE FOR RESIDUE AMP D 82

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JWB)

(-) Exons   (0, 0)

(no "Exon" information available for 1JWB)

(-) 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 B from PDB  Type:PROTEIN  Length:240
 aligned with MOEB_ECOLI | P12282 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           MOEB_ECOLI     2 AELSDQEMLRYNRQIILRGFDFDGQEALKDSRVLIVGLGGLGCAASQYLASAGVGNLTLLDFDTVSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPVNALLDDAELAALIAEHDLVLDCTDNVAVRNQLNAGCFAAKVPLVSGAAIRMEGQITVFTYQDGEPCYRCLSRLFGENALTCVEAGVMAPLIGVIGSLQAMEAIKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG 248
               SCOP domains d1jwbb_ B: Molybdenum cofactor biosynthesis protein MoeB                                                                                                                                                                                                SCOP domains
               CATH domains 1jwbB00 B:2-248 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------ThiF-1jwbB01 B:30-164                                                                                                                  ---MoeZ_MoeB-1jwb       B02 B:168-248                                                Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhhhhhheeeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.......hhhhhhh...-------....hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwb B   2 AELSDQEMLRYNRQIILRGFDFDGQEALKDSRVLIVGLGGLGCAASQYLASAGVGNLTLLDFDTVSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPVNALLDDAELAALIAEHDLVLDCTDNVAVRNQLNAGCFAAKVPLVSGAAIRMEGQITVFTYQDGEPCYRCLSRLFG-------EAGVMAPLIGVIGSLQAMEAIKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCEVCG 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
                                                                                                                                                                                                             181     189                                                           

Chain D from PDB  Type:PROTEIN  Length:80
 aligned with MOAD_ECOLI | P30748 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:80
                                    11        21        31        41        51        61        71        81
           MOAD_ECOLI     2 IKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
               SCOP domains d1jwbd_ D: Molybdopterin synthase subunit MoaD                                   SCOP domains
               CATH domains 1jwbD00 D:2-81  [code=3.10.20.30, no name defined]                               CATH domains
               Pfam domains --ThiS-1jwbD01 D:4-81                                                            Pfam domains
         Sec.struct. author .eeeehhhhhhhhh..eee.......hhhhhhhhhh.hhhhhhhh.....eeee..eee...........eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1jwb D   2 IKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
                                    11        21        31        41        51        61        71        81

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (13, 17)

Asymmetric Unit(hide GO term definitions)
Chain B   (MOEB_ECOLI | P12282)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0061605    molybdopterin-synthase adenylyltransferase activity    Catalysis of the reaction: ATP [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly = diphosphate [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain D   (MOAD_ECOLI | P30748)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MOAD_ECOLI | P307481fm0 1fma 1jw9 1jwa 1nvi 3bii
        MOEB_ECOLI | P122821jw9 1jwa

(-) Related Entries Specified in the PDB File

1fmo STRUCTURE OF MOLYBDOPTERIN SYNTHASE (MOAD IN COMPLEX WITH MOAE)
1jw9 STRUCTURE OF THE NATIVE MOEB-MOAD PROTEIN COMPLEX
1jwa STRUCTURE OF THE ATP-BOUND MOEB-MOAD PROTEIN COMPLEX