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(-) Description

Title :  DELETION MUTANT (DELTA 141) 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 :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Deletion Mutant, 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 2
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 0-139
    GeneMOAE OR CHLA5 OR B0785
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymMPT SYNTHASE SUBUNIT 2, MOLYBDOPTERIN SYNTHASE SUBUNIT 2, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E, MOLYBDOPTERIN CONVERTING FACTOR LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2GOL8Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL4Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL4Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH C:143 , HOH C:144 , HOH C:158 , GLY D:91 , NA D:142 , HOH D:156 , HOH D:158BINDING SITE FOR RESIDUE NA D 141
02AC2SOFTWAREHOH C:158 , HOH C:177 , NA D:141 , HOH D:156 , HOH D:158 , HOH D:199BINDING SITE FOR RESIDUE NA D 142
03AC3SOFTWAREHOH A:161 , HOH A:175 , HOH A:176 , GLY B:91 , HOH B:169BINDING SITE FOR RESIDUE NA B 141
04AC4SOFTWAREHOH A:193 , HOH E:154 , GLY F:91 , HOH F:168 , HOH F:183BINDING SITE FOR RESIDUE NA F 141
05AC5SOFTWARESER A:105 , PHE A:108 , GLN B:112 , ASP B:116 , HOH B:147 , ARG C:73 , TRP C:74BINDING SITE FOR RESIDUE GOL B 142
06AC6SOFTWAREGLN C:112 , ASP C:116 , HOH C:187 , HOH C:212 , SER D:105 , PHE D:108 , ARG E:73 , TRP E:74BINDING SITE FOR RESIDUE GOL C 141
07AC7SOFTWAREARG A:39 , HIS B:103 , ARG B:104 , SER B:105BINDING SITE FOR RESIDUE GOL B 143
08AC8SOFTWAREGLU A:27 , ASP A:28 , PRO A:75 , SER A:101 , ALA A:102BINDING SITE FOR RESIDUE GOL A 141
09AC9SOFTWAREGLY D:9 , GLN D:11 , PHE D:13 , ILE D:82 , ARG D:84 , HOH D:161BINDING SITE FOR RESIDUE GOL D 143
10BC1SOFTWAREGLU D:27 , ASP D:28 , PRO D:75 , GLY D:77 , SER D:101 , ALA D:102BINDING SITE FOR RESIDUE GOL D 144
11BC2SOFTWAREGLU A:24 , ARG A:78 , PRO E:20 , GLU E:24BINDING SITE FOR RESIDUE GOL A 142
12BC3SOFTWAREVAL B:7 , TYR D:55 , TRP D:125 , TRP D:136 , VAL D:137BINDING SITE FOR RESIDUE GOL D 145
13BC4SOFTWAREGLY C:36 , ARG C:39 , MET C:115 , HOH C:214 , ARG D:104 , ASN E:72BINDING SITE FOR RESIDUE FMT C 142
14BC5SOFTWAREARG A:104 , HOH A:155 , PHE B:34 , GLY B:36 , ARG B:39BINDING SITE FOR RESIDUE FMT A 143
15BC6SOFTWAREARG E:104 , GLY F:36 , ARG F:39 , LYS F:119 , HOH F:148BINDING SITE FOR RESIDUE FMT F 142
16BC7SOFTWAREPHE E:34 , GLY E:36 , ARG E:39 , ARG F:104BINDING SITE FOR RESIDUE FMT E 141
17BC8SOFTWAREHIS B:83 , LYS B:119 , PHE B:124BINDING SITE FOR RESIDUE FMT B 144
18BC9SOFTWAREPHE D:34 , GLY D:36 , ARG D:39 , LYS D:119 , HOH D:163BINDING SITE FOR RESIDUE FMT D 146

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NVJ)

(-) 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 A from PDB  Type:PROTEIN  Length:118
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
               SCOP domains d1nvja_ A: Molybdopterin synthase subu        nit MoaE                                                                         SCOP domains
               CATH domains 1nvjA00 A:2-127  [code=3.90.1170.40, n        o name defined]                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee..--------..eeeee..hhhhhhhhhhhhhhhhhh....eeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvj A   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVR--------NALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
                                    11        21        31       | -      | 51        61        71        81        91       101       111       121      
                                                                39       48                                                                               

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
               SCOP domains d1nvjb_ B: Molybdopterin synthase subunit MoaE                                                                                 SCOP domains
               CATH domains 1nvjB00 B:2-127  [code=3.90.1170.40, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee............eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvj B   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
                                    11        21        31        41        51        61        71        81        91       101       111       121      

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKRE 128
               SCOP domains d1nvjc_ C: Molybdopterin synthase subunit M   oaE                                                                               SCOP domains
               CATH domains 1nvjC00 C:2-128  [code=3.90.1170.40, no nam   e defined]                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee.hhhhh.---..eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nvj C   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLG---NALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKRE 128
                                    11        21        31        41  |   | 51        61        71        81        91       101       111       121       
                                                                     44  48                                                                                

Chain D from PDB  Type:PROTEIN  Length:135
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:139
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKREATPEGDRWVEAR 140
               SCOP domains d1nvjd_ D: Molybdopterin synthase subunit     MoaE                                                                                          SCOP domains
               CATH domains 1nvjD00 D:2-140  [code=3.90.1170.40, no n    ame defined]                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee.....----...eeee...hhhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh..eeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nvj D   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHN----VNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKREATPEGDRWVEAR 140
                                    11        21        31        41|    |  51        61        71        81        91       101       111       121       131         
                                                                   42   47                                                                                             

Chain E from PDB  Type:PROTEIN  Length:118
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWK 126
               SCOP domains d1nvje_ E: Molybdopterin synthase subun       it MoaE                                                                         SCOP domains
               CATH domains 1nvjE00 E:2-126  [code=3.90.1170.40, no        name defined]                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee...-------..eeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nvj E   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRN-------NALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWK 126
                                    11        21        31        |-      | 51        61        71        81        91       101       111       121     
                                                                 40      48                                                                              

Chain F from PDB  Type:PROTEIN  Length:119
 aligned with MOAE_ECOLI | P30749 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           MOAE_ECOLI     2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRNHNLGDSVNALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
               SCOP domains d1nvjf_ F: Molybdopterin synthase subun       it MoaE                                                                          SCOP domains
               CATH domains 1nvjF00 F:2-127  [code=3.90.1170.40, no        name defined]                                                                   CATH domains
           Pfam domains (1) ---MoaE-1nvjF01 F:5-122                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) ---MoaE-1nvjF02 F:5-122                                                                                                  ----- Pfam domains (2)
           Pfam domains (3) ---MoaE-1nvjF03 F:5-122                                                                                                  ----- Pfam domains (3)
           Pfam domains (4) ---MoaE-1nvjF04 F:5-122                                                                                                  ----- Pfam domains (4)
           Pfam domains (5) ---MoaE-1nvjF05 F:5-122                                                                                                  ----- Pfam domains (5)
           Pfam domains (6) ---MoaE-1nvjF06 F:5-122                                                                                                  ----- Pfam domains (6)
         Sec.struct. author ..eeeeee....hhhhhhhhhh......eeeeeeee...-------..eeeee..hhhhhhhhhhhhhhhh...eeeeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvj F   2 AETKIVVGPQPFSVGEEYPWLAERDEDGAVVTFTGKVRN-------NALTLEHYPGMTEKALAEIVDEARNRWPLGRVTVIHRIGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWKR 127
                                    11        21        31        |-      | 51        61        71        81        91       101       111       121      
                                                                 40      48                                                                               

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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
        MOAE_ECOLI | P307491fm0 1fma 1nvi 3bii

(-) Related Entries Specified in the PDB File

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