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(-) Description

Title :  CRYSTAL STRUCTURE OF MOAB PROTEIN AT 1.6 A RESOLUTION.
 
Authors :  R. Sanishvili, T. Skarina, A. Joachimiak, A. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  29 Aug 02  (Deposition) - 22 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mad, Weak Anomalous Signal, Molybdopterin Synthesis, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sanishvili, S. Beasley, T. Skarina, D. Glesne, A. Joachimiak, A. Edwards, A. Savchenko
The Crystal Structure Of Escherichia Coli Moab Suggests A Probable Role In Molybdenum Cofactor Synthesis.
J. Biol. Chem. V. 279 42139 2004
PubMed-ID: 15269205  |  Reference-DOI: 10.1074/JBC.M407694200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MOAB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO47Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:78 , THR A:79 , GLY A:80 , ASP A:85 , SER A:121 , PRO A:137 , GLY A:138 , HOH A:1252 , HOH A:1255BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWARESER A:19 , ASN A:20 , ARG A:21 , GLU A:52BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:12 , GLN A:71 , LYS A:170 , GLY A:171BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWARELYS A:130 , LEU A:168 , LYS A:169 , LYS A:170 , HOH A:1260BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY B:78 , THR B:79 , GLY B:80 , ASP B:85 , SER B:121 , PRO B:137 , GLY B:138 , HOH B:1243 , HOH B:1268 , HOH B:1284BINDING SITE FOR RESIDUE SO4 B 401
06AC6SOFTWARESER B:19 , ASN B:20 , ARG B:21 , GLU B:52BINDING SITE FOR RESIDUE SO4 B 402
07AC7SOFTWAREARG B:12 , GLU B:24 , GLN B:71 , LYS B:170 , GLY B:171BINDING SITE FOR RESIDUE SO4 B 403
08AC8SOFTWAREASP A:46 , TRP A:64 , SER A:67 , ASP A:69BINDING SITE FOR RESIDUE ACY A 1201
09AC9SOFTWAREASP B:46 , TRP B:64 , SER B:67 , ASP B:69BINDING SITE FOR RESIDUE ACY B 1202
10BC1SOFTWAREGLN B:38 , HIS B:43 , VAL B:44BINDING SITE FOR RESIDUE ACY B 1203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:160 -Pro A:161
2Arg B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOCF_BIOSYNTHESIS_1PS01078 Molybdenum cofactor biosynthesis proteins signature 1.MOAB_ECO5772-85
 		  2A:72-85
B:72-85
MOAB_ECOLI72-85
 		  2A:72-85
B:72-85

(-) Exons   (0, 0)

(no "Exon" information available for 1MKZ)

(-) 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:170
 aligned with MOAB_ECO57 | P0AF00 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:170
                                                                                                                                                                                                 170  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       | -
           MOAB_ECO57     3 QVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRMLSFEEIGTSTLQSRAVAGVANKTLIFAMPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKK--   -
               SCOP domains d1mkza_ A: MoaB                                                                                                                                                            SCOP domains
               CATH domains 1mkzA00 A:3-172 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhh.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------MOCF_BIOSYNTHE--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkz A   3 QVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRmLSFEEIGTSTLQSRAVAGVANKTLILAmPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKKGS 172
                                    12        22        32        42        52        62        72        82        92       102     | 112       122       132   |   142       152       162       172
                                                                                                                                   108-MSE                     136-MSE                                


Chain A from PDB  Type:PROTEIN  Length:170
 aligned with MOAB_ECOLI | P0AEZ9 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:170
                                                                                                                                                                                                 170  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       | -
           MOAB_ECOLI     3 QVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRMLSFEEIGTSTLQSRAVAGVANKTLIFAMPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKK--   -
               SCOP domains d1mkza_ A: MoaB                                                                                                                                                            SCOP domains
               CATH domains 1mkzA00 A:3-172 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhh.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------MOCF_BIOSYNTHE--------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkz A   3 QVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRmLSFEEIGTSTLQSRAVAGVANKTLILAmPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKKGS 172
                                    12        22        32        42        52        62        72        82        92       102     | 112       122       132   |   142       152       162       172
                                                                                                                                   108-MSE                     136-MSE                                


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with MOAB_ECO57 | P0AF00 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:171
                                                                                                                                                                                                  170  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        |- 
           MOAB_ECO57     2 SQVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRMLSFEEIGTSTLQSRAVAGVANKTLIFAMPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKK--   -
               SCOP domains d1mkzb_ B: MoaB                                                                                                                                                             SCOP domains
               CATH domains 1mkzB00 B:2-172 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                             CATH domains
           Pfam domains (1) ----------MoCF_biosynth-1mkzB01 B:12-157                                                                                                                    --------------- Pfam domains (1)
           Pfam domains (2) ----------MoCF_biosynth-1mkzB02 B:12-157                                                                                                                    --------------- Pfam domains (2)
         Sec.struct. author ..........eeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhh.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------MOCF_BIOSYNTHE--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkz B   2 SQVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRmLSFEEIGTSTLQSRAVAGVANKTLILAmPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKKGS 172
                                    11        21        31        41        51        61        71        81        91       101      |111       121       131    |  141       151       161       171 
                                                                                                                                    108-MSE                     136-MSE                                


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with MOAB_ECOLI | P0AEZ9 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:171
                                                                                                                                                                                                  170  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        |- 
           MOAB_ECOLI     2 SQVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRMLSFEEIGTSTLQSRAVAGVANKTLIFAMPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKK--   -
               SCOP domains d1mkzb_ B: MoaB                                                                                                                                                             SCOP domains
               CATH domains 1mkzB00 B:2-172 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                             CATH domains
           Pfam domains (1) ----------MoCF_biosynth-1mkzB01 B:12-157                                                                                                                    --------------- Pfam domains (1)
           Pfam domains (2) ----------MoCF_biosynth-1mkzB02 B:12-157                                                                                                                    --------------- Pfam domains (2)
         Sec.struct. author ..........eeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhh.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------MOCF_BIOSYNTHE--------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkz B   2 SQVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVEGFGEVFRmLSFEEIGTSTLQSRAVAGVANKTLILAmPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKKGS 172
                                    11        21        31        41        51        61        71        81        91       101      |111       121       131    |  141       151       161       171 
                                                                                                                                    108-MSE                     136-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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MOAB_ECO57 | P0AF00)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.

Chain A,B   (MOAB_ECOLI | P0AEZ9)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0061598    molybdopterin adenylyltransferase activity    Catalysis of the reaction ATP + molybdopterin = diphosphate + adenylyl-molybdopterin.
    GO:0061599    molybdopterin molybdotransferase activity    Catalysis of the reaction adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP.
    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.
    GO:0018315    molybdenum incorporation into molybdenum-molybdopterin complex    The incorporation of molybdenum into a molybdenum-molybdopterin complex.
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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  1mkz
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 Related Entries

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

UniProtKB/Swiss-Prot
        MOAB_ECO57 | P0AF00: 1r2k
        MOAB_ECOLI | P0AEZ9: 1r2k

(-) Related Entries Specified in the PDB File

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