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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT (MOCS2B)
 
Authors :  M. Vollmar, W. Kiyani, T. Krojer, S. Goubin, C. Allerston, D. S. Froese, F. Von Delft, N. Burgess-Brown, C. Bountra, C. H. Arrowsmith, A. Edwa W. W. Yue
Date :  30 Mar 12  (Deposition) - 29 Aug 12  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),D (1x)
Biol. Unit 2:  A (1x),D (1x)
Biol. Unit 3:  B (1x),C (1x)
Biol. Unit 4:  B (1x),C (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vollmar, W. Kiyani, T. Krojer, S. Goubin, C. Allerston, D. S. Froese F. Von Delft, N. Burgess-Brown, C. Bountra, C. H. Arrowsmith, A. Edwards, W. W. Yue
Crystal Structure Of Human Molybdopterin Synthase Catalytic Subunit (Mocs2B)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
    ChainsA, B, C, D
    EC Number2.8.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentCATALYTIC SUBUNIT RESIDUES 38-172
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMOCO1-B, MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2 LARGE SUBUNIT, MOLYBDENUM COFACTOR SYNTHESIS PROTEIN 2B, MOCS2B, MOLYBDOPTERIN-SYNTHASE LARGE SUBUNIT, MPT SYNTHASE LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A (1x)  D (1x)
Biological Unit 2 (1x)A (1x)  D (1x)
Biological Unit 3 (1x) B (1x)C (1x) 
Biological Unit 4 (1x) B (1x)C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:143 , ARG B:144 , ARG C:79BINDING SITE FOR RESIDUE GOL B1172
2AC2SOFTWAREHIS C:143 , ARG C:144BINDING SITE FOR RESIDUE GOL C1172
3AC3SOFTWAREARG A:79 , HIS D:143 , ARG D:144BINDING SITE FOR RESIDUE GOL D1173
4AC4SOFTWAREHIS A:143 , ARG A:144 , ARG D:79BINDING SITE FOR RESIDUE GOL A1172
5AC5SOFTWAREGLU A:100 , HOH A:2029BINDING SITE FOR RESIDUE EDO A1173
6AC6SOFTWARELEU A:54 , SER A:55 , GLU A:58 , PHE A:122BINDING SITE FOR RESIDUE EDO A1174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AP8)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:96 -Pro A:97
2Leu B:96 -Pro B:97
3Leu C:96 -Pro C:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 16)

Asymmetric Unit (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050091T50AMOC2B_HUMANPolymorphism2233213A/B/C/DT50A
2UniProtVAR_050092T77AMOC2B_HUMANPolymorphism2233215A/B/C/DT77A
3UniProtVAR_050093H123YMOC2B_HUMANPolymorphism2233218A/B/C/DH123Y
4UniProtVAR_012765E168KMOC2B_HUMANDisease (MOCODB)121908605A/B/C/DE168K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050091T50AMOC2B_HUMANPolymorphism2233213A/DT50A
2UniProtVAR_050092T77AMOC2B_HUMANPolymorphism2233215A/DT77A
3UniProtVAR_050093H123YMOC2B_HUMANPolymorphism2233218A/DH123Y
4UniProtVAR_012765E168KMOC2B_HUMANDisease (MOCODB)121908605A/DE168K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050091T50AMOC2B_HUMANPolymorphism2233213A/DT50A
2UniProtVAR_050092T77AMOC2B_HUMANPolymorphism2233215A/DT77A
3UniProtVAR_050093H123YMOC2B_HUMANPolymorphism2233218A/DH123Y
4UniProtVAR_012765E168KMOC2B_HUMANDisease (MOCODB)121908605A/DE168K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050091T50AMOC2B_HUMANPolymorphism2233213B/CT50A
2UniProtVAR_050092T77AMOC2B_HUMANPolymorphism2233215B/CT77A
3UniProtVAR_050093H123YMOC2B_HUMANPolymorphism2233218B/CH123Y
4UniProtVAR_012765E168KMOC2B_HUMANDisease (MOCODB)121908605B/CE168K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050091T50AMOC2B_HUMANPolymorphism2233213B/CT50A
2UniProtVAR_050092T77AMOC2B_HUMANPolymorphism2233215B/CT77A
3UniProtVAR_050093H123YMOC2B_HUMANPolymorphism2233218B/CH123Y
4UniProtVAR_012765E168KMOC2B_HUMANDisease (MOCODB)121908605B/CE168K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AP8)

(-) Exons   (0, 0)

(no "Exon" information available for 4AP8)

(-) 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:134
 aligned with MOC2B_HUMAN | O96007 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:134
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    
          MOC2B_HUMAN    38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
               SCOP domains d4ap8a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhh......eeeeeeee...ee..eeeeeeeeeeeehhhhhhhhhhhhhhhhhh.eeeeeeeee.eeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------A--------------------------A---------------------------------------------Y--------------------------------------------K--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap8 A  38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with MOC2B_HUMAN | O96007 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:134
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    
          MOC2B_HUMAN    38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
               SCOP domains d4ap8b_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhh......eeeeeeee...ee..eeeeeeeeee..hhhhhhhhhhhhhhhhhh....eeeeee.eeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------A--------------------------A---------------------------------------------Y--------------------------------------------K--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap8 B  38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with MOC2B_HUMAN | O96007 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:134
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    
          MOC2B_HUMAN    38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
               SCOP domains d4ap8c_ C: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhh......eeeeeeee...ee..eeeeeeeeeeeehhhhhhhhhhhhhhhhhh.eeeeeeeee.eeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------A--------------------------A---------------------------------------------Y--------------------------------------------K--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap8 C  38 EVEEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYE 171
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    

Chain D from PDB  Type:PROTEIN  Length:133
 aligned with MOC2B_HUMAN | O96007 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:133
                                    49        59        69        79        89        99       109       119       129       139       149       159       169   
          MOC2B_HUMAN    40 EEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYEE 172
               SCOP domains d4ap8d_ D: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhh......eeeeeeee...ee..ee..eeeeeehhhhhhhhhhhhhhhhhhhh.eeeeeeeee.eeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------A--------------------------A---------------------------------------------Y--------------------------------------------K---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ap8 D  40 EEKSKDVINFTAEKLSVDEVSQLVISPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASLEAVSYAIDTLKAKVPIWKKEIYEE 172
                                    49        59        69        79        89        99       109       119       129       139       149       159       169   

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AP8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AP8)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MOC2B_HUMAN | O96007)
molecular function
    GO:0030366    molybdopterin synthase activity    Catalysis of the conversion of precursor Z to molybdopterin, the final step in molybdopterin biosynthesis.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019008    molybdopterin synthase complex    A protein complex that possesses molybdopterin synthase activity. In E. coli, the complex is a heterotetramer consisting of two MoaD and two MoaE subunits.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        MOC2B_HUMAN | O960075mpo

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