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(-) Description

Title :  CRYSTAL STRUCTURE OF MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Nov 04  (Deposition) - 07 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Moea Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Kunishima
Crystal Structure Of Molybdopterin Biosynthesis Moea Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 CODON PLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: MOEA PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WU2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WU2)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ile A:50 -Pro A:51
2Lys A:282 -Pro A:283
3Lys A:361 -Gly A:362
4Ile B:50 -Pro B:51
5Lys B:282 -Pro B:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WU2)

(-) Exons   (0, 0)

(no "Exon" information available for 1WU2)

(-) Sequences/Alignments

Asymmetric/Biological 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:383
 aligned with O59354_PYRHO | O59354 from UniProtKB/TrEMBL  Length:396

    Alignment length:391
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
         O59354_PYRHO     6 KLVPYREALKLLLDDINEIEDTEKVPLREAVGRVLAEDIVTEFDIPPFDRAAVDGYAIRAEDTFQAREYNPIELTVIEEVPAGNVAKEEVTTGKAIKVLTGTRIPKGANAVIMQEMVKREGDKIYVLRPVAPGQNIAFTGEDVKKGEVVLRKGTILRPQDVAMLKALGIKKVPVKVKPKVGIIITGSELIEEPSEEGFKEGKIVETNSIMLQGLVEKFFGEPILYGVLPDDESIIKETLEKAKNECDIVLITGGSAFGDKDYAHKFVNLLFHGTTIKPGRPFGYGEKVFIMSGYPVSVFAQFNLFVKHALAKMVGAQNYEVKVKAILQDDIPSQLGRYEFIKIYYENGIARVIKKKGSGILSSLLASNAYLEIPEDSEGYRRGEEVWITLY 396
               SCOP domains d1wu2a2 A:6-180 Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains                                                                                   d1wu2a3 A:181-324 MoeA, central domain                                                                                                          d1wu2a1 A:325-396                                                        SCOP domains
               CATH domains 1wu2A01              1wu2A02                1wu2A03 A:50-148 Molybdopterin biosynthesis moea protein, domain 3.                                1wu2A02 A:27-49,A:149-181        1wu2A01 A:6-26,A:182-319 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                  1wu2A04 A:320-396 MoeA C-terminal domain-like                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....eeeee.hhh........ee.........ee...eeeehhhhhh.......eeeeeeee..............eeeee...........eeee.hhheee..eeee.........ee..........eee......hhhhhhhhhhh...eeeee...eeeeeee...ee...hhhhhhh..ee.hhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh.eeee..--------..........ee...ee.....eee..eee...hhhhhhhhhhhhhhhhhhhhhh......eeeeee...ee.....eeeeeeeee..eeee........hhhhhhh.eeeee.....ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu2 A   6 KLVPYREALKLLLDDINEIEDTEKVPLREAVGRVLAEDIVTEFDIPPFDRAAVDGYAIRAEDTFQAREYNPIELTVIEEVPAGNVAKEEVTTGKAIKVLTGTRIPKGANAVImQEmVKREGDKIYVLRPVAPGQNIAFTGEDVKKGEVVLRKGTILRPQDVAmLKALGIKKVPVKVKPKVGIIITGSELIEEPSEEGFKEGKIVETNSImLQGLVEKFFGEPILYGVLPDDESIIKETLEKAKNECDIVLIT--------DYAHKFVNLLFHGTTIKPGRPFGYGEKVFImSGYPVSVFAQFNLFVKHALAKmVGAQNYEVKVKAILQDDIPSQLGRYEFIKIYYENGIARVIKKKGSGILSSLLASNAYLEIPEDSEGYRRGEEVWITLY 396
                                    15        25        35        45        55        65        75        85        95       105       115  |  | 125       135       145       155       165  |    175       185       195       205       215       225       235       245       255 |       -|      275       285       295|      305       315  |    325       335       345       355       365       375       385       395 
                                                                                                                                          118-MSE                                           168-MSE                                        215-MSE                                   257      266                           296-MSE               318-MSE                                                                          
                                                                                                                                             121-MSE                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:379
 aligned with O59354_PYRHO | O59354 from UniProtKB/TrEMBL  Length:396

    Alignment length:391
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395 
         O59354_PYRHO     6 KLVPYREALKLLLDDINEIEDTEKVPLREAVGRVLAEDIVTEFDIPPFDRAAVDGYAIRAEDTFQAREYNPIELTVIEEVPAGNVAKEEVTTGKAIKVLTGTRIPKGANAVIMQEMVKREGDKIYVLRPVAPGQNIAFTGEDVKKGEVVLRKGTILRPQDVAMLKALGIKKVPVKVKPKVGIIITGSELIEEPSEEGFKEGKIVETNSIMLQGLVEKFFGEPILYGVLPDDESIIKETLEKAKNECDIVLITGGSAFGDKDYAHKFVNLLFHGTTIKPGRPFGYGEKVFIMSGYPVSVFAQFNLFVKHALAKMVGAQNYEVKVKAILQDDIPSQLGRYEFIKIYYENGIARVIKKKGSGILSSLLASNAYLEIPEDSEGYRRGEEVWITLY 396
               SCOP domains d1wu2b2 B:6-180 Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains                                                                                   d1wu2b3 B:181-324 MoeA, central domain                                                                                                          d1wu2b1 B:325-396                                                        SCOP domains
               CATH domains 1wu2B01         1wu2B02 B:22-48,B:149-181  1wu2B03 B:49-148 Molybdopterin biosynthesis moea protein, domain 3.                                 1wu2B02 B:22-48,B:149-181        1wu2B01 B:6-21,B:182-325 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                        1wu2B04 B:326-396 MoeA C-terminal domain-like                           CATH domains
           Pfam domains (1) -MoeA_N-1wu2B05 B:7-173                                                                                                                                                 ------------MoCF_biosynth-1wu2B01 B:186-336                                                                                                                        ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -MoeA_N-1wu2B06 B:7-173                                                                                                                                                 ------------MoCF_biosynth-1wu2B02 B:186-336                                                                                                                        ------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MoeA_C-1wu2B03 B:329-396                                             Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MoeA_C-1wu2B04 B:329-396                                             Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhh.....eeeee.hhh........ee.........ee...eeeehhhhhh.......eeeeeeee..............eeeee...........eeee.hhhee...eeee.........ee..........eee......hhhhhhhhhhh...eeeee...eeeeee....ee.....hhhhhh.ee.hhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh.eeeee.------------.....ee...ee.....eee..eeee..hhhhhhhhhhhhhhhhhhhhhh......eeeeee...ee.....eeeeeeeee..eeee........hhhhhh..eeeee.....ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu2 B   6 KLVPYREALKLLLDDINEIEDTEKVPLREAVGRVLAEDIVTEFDIPPFDRAAVDGYAIRAEDTFQAREYNPIELTVIEEVPAGNVAKEEVTTGKAIKVLTGTRIPKGANAVImQEmVKREGDKIYVLRPVAPGQNIAFTGEDVKKGEVVLRKGTILRPQDVAmLKALGIKKVPVKVKPKVGIIITGSELIEEPSEEGFKEGKIVETNSImLQGLVEKFFGEPILYGVLPDDESIIKETLEKAKNECDIVLITG------------FVNLLFHGTTIKPGRPFGYGEKVFImSGYPVSVFAQFNLFVKHALAKmVGAQNYEVKVKAILQDDIPSQLGRYEFIKIYYENGIARVIKKKGSGILSSLLASNAYLEIPEDSEGYRRGEEVWITLY 396
                                    15        25        35        45        55        65        75        85        95       105       115  |  | 125       135       145       155       165  |    175       185       195       205       215       225       235       245       255  |      -     | 275       285       295|      305       315  |    325       335       345       355       365       375       385       395 
                                                                                                                                          118-MSE                                           168-MSE                                        215-MSE                                    258          271                      296-MSE               318-MSE                                                                          
                                                                                                                                             121-MSE
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MoCF_biosynth] (31)
(-)
Clan: no clan defined [family: MoeA_C] (15)
(-)
Clan: no clan defined [family: MoeA_N] (15)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O59354_PYRHO | O59354)
biological process
    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.

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    Lys A:282 - Pro A:283   [ RasMol ]  
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