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(-) Description

Title :  ORTHORHOMBIC CRYSTAL FORM OF MOLYBDOPTERIN SYNTHASE
 
Authors :  M. J. Rudolph, M. M. Wuebbens, O. Turque, K. V. Rajagopalan, H. Schindel
Date :  03 Feb 03  (Deposition) - 06 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  D,E
Biol. Unit 1:  D,E  (2x)
Keywords :  Protein-Protein Complex, Molybdenum Cofactor Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Rudolph, M. M. Wuebbens, O. Turque, K. V. Rajagopalan, H. Schindelin
Structural Studies Of Molybdopterin Synthase Provide Insights Into Its Catalytic Mechanism
J. Biol. Chem. V. 278 14514 2003
PubMed-ID: 12571227  |  Reference-DOI: 10.1074/JBC.M300449200

(-) Compounds

Molecule 1 - MOLYBDOPTERIN CONVERTING FACTOR SUBUNIT 1
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MOLYBDOPTERIN SYNTHASE - SMALL SUBUNIT
    Gene: MOAD OR CHLA4 OR CHLM OR B0784
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MPT SYNTHASE SUBUNIT 1, MOLYBDOPTERIN SYNTHASE SUBUNIT 1, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D, MOLYBDOPTERIN CONVERTING FACTOR SMALL SUBUNIT
 
Molecule 2 - MOLYBDOPTERIN CONVERTING FACTOR SUBUNIT 2
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MOLYBDOPTERIN SYNTHASE - LARGE SUBUNIT
    Gene: MOAE OR CHLA5 OR B0785
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MPT SYNTHASE SUBUNIT 2, MOLYBDOPTERIN SYNTHASE SUBUNIT 2, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E, MOLYBDOPTERIN CONVERTING FACTOR LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : DE
Biological Unit 1 (2x): DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:103 , ARG E:104 , LYS E:119 , HOH E:170 , HOH E:196 , HOH E:219 , HOH E:246BINDING SITE FOR RESIDUE SO4 E 151
2AC2SOFTWARESER D:61 , PHE D:62 , HOH D:92 , HOH D:144 , LYS E:148 , HOH E:261BINDING SITE FOR RESIDUE SO4 D 82
3AC3SOFTWAREVAL D:60 , SER D:61 , HIS D:64 , HOH D:131BINDING SITE FOR RESIDUE SO4 D 83
4AC4SOFTWARESER D:39 , ASP D:40 , ARG D:41BINDING SITE FOR RESIDUE GOL D 84
5AC5SOFTWAREASN D:56 , HIS D:64 , HOH D:95 , HOH D:100BINDING SITE FOR RESIDUE GOL D 85

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NVI)

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

    Alignment length:81
                                    10        20        30        40        50        60        70        80 
           MOAD_ECOLI     1 MIKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
               SCOP domains d1nvid_ D: Molybdopterin synthase subunit MoaD                                    SCOP domains
               CATH domains 1nviD00 D:1-81  [code=3.10.20.30, no name defined]                                CATH domains
               Pfam domains ---ThiS-1nviD01 D:4-81                                                            Pfam domains
         Sec.struct. author .eeeeehhhhhhhhh..eeee.....hhhhhhhhhhh.hhhhhhhhh....eeee..ee...........eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1nvi D   1 MVKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGG  81
                                    10        20        30        40        50        60        70        80 


Chain E from PDB  Type:PROTEIN  Length:142
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKREATPEGDRWVEARESDQQAAKRW 150
               SCOP domains d1nvie_ E: Molybdopterin synthase subu       nit MoaE                                                                                                 SCOP domains
               CATH domains 1nviE00 E:2-150  [code=3.90.1170.40, n       o name defined]                                                                                          CATH domains
               Pfam domains ---MoaE-1nviE01 E:5-122                                                                                                  ---------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhh.....eeeeeeee..-------...eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeee......ee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nvi E   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVR-------VNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKREATPEGDRWVEARESDQQAAKRW 150
                                    11        21        31       | -     |  51        61        71        81        91       101       111       121       131       141         
                                                                39      47
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)
(-)
Clan: no clan defined [family: MoaE] (7)

(-) Gene Ontology  (7, 10)

Asymmetric Unit(hide GO term definitions)
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.

Chain E   (MOAE_ECOLI | P30749)
molecular function
    GO:0030366    molybdopterin synthase activity    Catalysis of the conversion of precursor Z to molybdopterin, the final step in molybdopterin biosynthesis.
    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: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.
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:0032324    molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) 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 | P30748: 1fm0 1fma 1jw9 1jwa 1jwb 3bii
        MOAE_ECOLI | P30749: 1fm0 1fma 1nvj 3bii

(-) Related Entries Specified in the PDB File

1fm0 MONOCLINIC CRYSTAL FORM OF MOLYBDOPTERIN SYNTHASE
1fma MONOCLINIC CRYSTAL FORM OF MOLYBDOPTERIN SYNTHASE - COVALENT COMPLEX