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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVATED MPT SYNTHASE
 
Authors :  J. N. Daniels, H. Schindelin
Date :  30 Nov 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  D,E
Biol. Unit 1:  D,E  (2x)
Keywords :  Mpt Synthase, Moco Biosynthesis, Moae, Moad, Ubiquitin-Like, Beta-Hammerhead Fold, Molybdenum Cofactor Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Daniels, M. M. Wuebbens, K. V. Rajagopalan, H. Schindelin
Crystal Structure Of A Molybdopterin Synthase-Precursor Z Complex: Insight Into Its Sulfur Transfer Mechanism And Its Role In Molybdenum Cofactor Deficiency.
Biochemistry V. 47 615 2008
PubMed-ID: 18092812  |  Reference-DOI: 10.1021/BI701734G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 1
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21 DE3
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MOAD, CHLA4, CHLM
    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
    Expression System Cell Line: BL21 DE3
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MOAE, CHLA5
    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
1CL4Ligand/IonCHLORIDE ION
2GL31Mod. Amino AcidTHIOGLYCIN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GL32Mod. Amino AcidTHIOGLYCIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN D:33 , HOH D:310 , HOH D:336 , TYR E:55 , GLY E:57BINDING SITE FOR RESIDUE CL D 303
2AC2SOFTWAREARG E:39 , ARG E:104BINDING SITE FOR RESIDUE CL E 301
3AC3SOFTWAREGLN E:112 , ARG E:149 , HOH E:316BINDING SITE FOR RESIDUE CL E 302
4AC4SOFTWAREARG E:39 , LEU E:50 , LYS E:126BINDING SITE FOR RESIDUE CL E 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BII)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BII)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BII)

(-) 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 d3biid_ D: Molybdopterin synthase subunit MoaD                                    SCOP domains
               CATH domains 3biiD00 D:1-80  [code=3.10.20.30, no name defined]                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhh..eeee.....hhhhhhhhhhh.hhhhhhhhh....eeee..ee...........eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bii D   1 MIKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTGg  81
                                    10        20        30        40        50        60        70        80|
                                                                                                           81-GL3


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 d3biie_ E: Molybdopterin synthase subu       nit MoaE                                                                                                 SCOP domains
               CATH domains 3biiE00 E:2-150  [code=3.90.1170.40, n       o name defined]                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee..-------...eeeee...hhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bii 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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  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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 1nvi
        MOAE_ECOLI | P30749: 1fm0 1fma 1nvi 1nvj

(-) Related Entries Specified in the PDB File

1fm0 MONOCLINIC CRYSTAL FORM OF E.COLI MOLYBDOPTERIN SYNTHASE
1fma MONOCLINIC CRYSTAL FORM OF E.COLI MOLYBDOPTERIN SYNTHASE - COVALENT COMPLEX
1nvi ORTHORHOMBIC FORM OF THE E.COLI MPT SYNTHASE
1nvj DELETION MUTANT (DELTA 141) OF MOLYBDOPTERIN SYNTHASE
2q5w MONOCLINIC FORM OF THE S.AUREUS MPT SYNTHASE
2qie ORTHORHOMBIC FORM OF THE S.AUREUS MPT SYNTHASE IN COMPLEX WITH PRECURSOR Z