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(-) Description

Title :  STAPHYLOCOCCUS AUREUS MOLYBDOPTERIN SYNTHASE IN COMPLEX WITH PRECURSOR Z
 
Authors :  J. N. Daniels, H. Schindelin
Date :  04 Jul 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,D,E,G,H,J,K
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  G,H,J,K  (1x)
Keywords :  Molybdopterin, Moco, Mpt Synthase, Moad, Moae, Transferase, Molybdenum Cofactor Biosynthesis, Beta-Grasp (Ubiquitin- Like), Alpha Beta Hammerhead Fold (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 2
    Chains: A, H, K, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MOAE
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: MPT SYNTHASE SUBUNIT 2, MOLYBDOPTERIN SYNTHASE SUBUNIT 2, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E, MOLYBDOPTERIN-CONVERTING FACTOR LARGE SUBUNIT
 
Molecule 2 - MOLYBDOPTERIN SYNTHASE SMALL SUBUNIT
    Chains: B, G, J, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MOAD
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABDEGHJK
Biological Unit 1 (1x): ABDE    
Biological Unit 2 (1x):     GHJK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
18CS4Ligand/Ion(2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
18CS2Ligand/Ion(2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
18CS2Ligand/Ion(2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , ARG A:36 , THR A:44 , LYS A:116 , LYS A:123 , GLU A:125 , HOH A:507 , HOH A:514 , GLY B:77 , GLY E:26 , PRO E:99 , HIS E:100 , ARG E:101BINDING SITE FOR RESIDUE 8CS A 501
2AC2SOFTWAREGLY A:26 , ALA A:27 , HIS A:100 , ARG A:101 , GLY D:77 , HIS E:34 , VAL E:35 , ARG E:36 , LYS E:40 , LEU E:47 , LYS E:116 , LYS E:123BINDING SITE FOR RESIDUE 8CS E 501
3AC3SOFTWAREGLY G:77 , HIS H:34 , ARG H:36 , LEU H:47 , LYS H:116 , LYS H:123 , GLU H:125 , HOH H:509 , GLY K:26 , ALA K:27 , PRO K:99 , HIS K:100 , ARG K:101BINDING SITE FOR RESIDUE 8CS H 501
4AC4SOFTWAREGLY H:26 , HIS H:100 , ARG H:101 , GLY J:77 , HIS K:34 , ARG K:36 , THR K:44 , LYS K:116 , LYS K:123 , GLU K:125 , HOH K:502BINDING SITE FOR RESIDUE 8CS K 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QIE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QIE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QIE)

(-) Exons   (0, 0)

(no "Exon" information available for 2QIE)

(-) 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:136
 aligned with MOAE_STAAN | P65401 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           MOAE_STAAN     1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
               SCOP domains d2qiea_ A: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhh.....eeeeeeee...ee..ee..eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeee....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qie A   1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain B from PDB  Type:PROTEIN  Length:77
 aligned with MOAD_STAAN | Q7A441 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:77
                                    10        20        30        40        50        60        70       
           MOAD_STAAN     1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhh..eee......eehhhhhhhhhhhhhhhh....eeee..ee.....ee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2qie B   1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
                                    10        20        30        40        50        60        70       


Chain D from PDB  Type:PROTEIN  Length:77
 aligned with MOAD_STAAN | Q7A441 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:77
                                    10        20        30        40        50        60        70       
           MOAD_STAAN     1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhh..eee......eehhhhhhhhhhhhhhhh....eeee..ee.....ee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2qie D   1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
                                    10        20        30        40        50        60        70       


Chain E from PDB  Type:PROTEIN  Length:136
 aligned with MOAE_STAAN | P65401 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           MOAE_STAAN     1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
               SCOP domains d2qiee_ E: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhh.....eeeeeeee...........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qie E   1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      


Chain G from PDB  Type:PROTEIN  Length:77
 aligned with MOAD_STAAN | Q7A441 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:77
                                    10        20        30        40        50        60        70       
           MOAD_STAAN     1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhh..eee......eehhhhhhhhhhhhhhhh....eeee..ee.....ee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2qie G   1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
                                    10        20        30        40        50        60        70       


Chain H from PDB  Type:PROTEIN  Length:131
 aligned with MOAE_STAAN | P65401 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           MOAE_STAAN     1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
               SCOP domains d2qieh_ H: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhh.....eeeeeeee...ee..ee...eeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeee.-----..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qie H   1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEI-----KWQGH 136
                                    10        20        30        40        50        60        70        80        90       100       110       120     |   - |    
                                                                                                                                                       126   132    


Chain J from PDB  Type:PROTEIN  Length:77
 aligned with MOAD_STAAN | Q7A441 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:77
                                    10        20        30        40        50        60        70       
           MOAD_STAAN     1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --ThiS-2qieJ01 J:3-77                                                         Pfam domains (1)
           Pfam domains (2) --ThiS-2qieJ02 J:3-77                                                         Pfam domains (2)
           Pfam domains (3) --ThiS-2qieJ03 J:3-77                                                         Pfam domains (3)
           Pfam domains (4) --ThiS-2qieJ04 J:3-77                                                         Pfam domains (4)
         Sec.struct. author .eee.hhhhhhhhh..eee......eehhhhhhhhhhhhhhhh....eeee..ee.....ee....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2qie J   1 MKVLYFAEIKDILQKAQEDIVLEQALTVQQFEDLLFERYPQINNKKFQVAVNEEFVQKSDFIQPNDTVALIPPVSGG  77
                                    10        20        30        40        50        60        70       


Chain K from PDB  Type:PROTEIN  Length:136
 aligned with MOAE_STAAN | P65401 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           MOAE_STAAN     1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
               SCOP domains d2qiek_ K: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MoaE-2qieK01 K:3-119                                                                                                 ----------------- Pfam domains (1)
           Pfam domains (2) --MoaE-2qieK02 K:3-119                                                                                                 ----------------- Pfam domains (2)
           Pfam domains (3) --MoaE-2qieK03 K:3-119                                                                                                 ----------------- Pfam domains (3)
           Pfam domains (4) --MoaE-2qieK04 K:3-119                                                                                                 ----------------- Pfam domains (4)
         Sec.struct. author ...eeee.....hhhhhhhhh.....eeeeeeee...ee..ee..eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeee....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qie K   1 MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QIE)

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (4, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,E,H,K   (MOAE_STAAN | P65401)
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.

Chain B,D,G,J   (MOAD_STAAN | Q7A441)
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.
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.

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  MOAE_STAAN | P65401
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 Related Entries

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

UniProtKB/Swiss-Prot
        MOAD_STAAN | Q7A441: 2q5w
        MOAE_STAAN | P65401: 2q5w

(-) Related Entries Specified in the PDB File

1fm0 E.COLI MOLYBDOPTERIN SYNTHASE (MOAD/MOAE)
1fma E.COLI MOLYBDOPTERIN SYNTHASE (MOAD/MOAE)- COVALENT COMPLEX
1nvi ORTHORHOMBIC CRYSTAL FORM OF E.COLI MOLYBDOPTERIN SYNTHASE
1nvj DELETION MUTANT (DELTA 141) OF E.COLI MOLYBDOPTERIN SYNTHASE
2q5w THE X-RAY CRYSTAL STRUCTURE OF MOLYBDOPTERIN SYNTHASE FROM STAPHYLOCOCCUS AUREUS
3bii E. COLI MOLYBDOPTERIN SYNTHASE- ACTIVATED