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(-) Description

Title :  PROTEIN-PROTEIN COMPLEX OF SUBUNIT 1 AND 2 OF MOLYBDOPTERIN-CONVERTING FACTOR FROM HELICOBACTER PYLORI 26695
 
Authors :  B. Nocek, A. Stein, N. Marshall, R. Jedrzejczak, G. Babnigg, A. Joachim Midwest Center For Structural Genomics (Mcsg)
Date :  26 Apr 11  (Deposition) - 29 Jun 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (2x)
Biol. Unit 2:  A,D  (1x)
Biol. Unit 3:  B,C  (2x)
Biol. Unit 4:  B,C  (1x)
Keywords :  Mcsg, Psi-Biology, Structural Genomics, Midwest Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, A. Stein, N. Marshall, R. Jedrzejczak, G. Babnigg, A. Joachimiak
Protein-Protein Complex Of Subunit 1 And 2 Of Molybdopterin-Converting Factor From Helicobacter Pylori 26695
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDOPTERIN SYNTHASE CATALYTIC SUBUNIT
    Chains: A, B
    EC Number: 2.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MOAE, HP_0800
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: MPT SYNTHASE SUBUNIT 2, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E, MOLYBDOPTERIN-CONVERTING FACTOR LARGE SUBUNIT, MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2
 
Molecule 2 - MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 1 (MOAD)
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HP_0801
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A  D
Biological Unit 2 (1x): A  D
Biological Unit 3 (2x):  BC 
Biological Unit 4 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 14)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (3, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:97 , ARG A:98 , HOH A:162 , HOH A:179BINDING SITE FOR RESIDUE SO4 A 146
2AC2SOFTWARETRP A:58 , ASN A:115 , LEU A:138 , HOH A:163 , LEU D:51BINDING SITE FOR RESIDUE EDO A 147
3AC3SOFTWAREILE A:50 , TYR A:51 , GLU A:52 , ALA A:53 , HOH A:166BINDING SITE FOR RESIDUE EDO A 148
4AC4SOFTWAREASN B:97 , ARG B:98 , LYS B:113 , HOH B:159 , HOH B:186 , HOH B:188BINDING SITE FOR RESIDUE SO4 B 146
5AC5SOFTWAREALA B:131 , LYS B:132 , GLU B:133 , ARG B:134BINDING SITE FOR RESIDUE EDO B 147
6AC6SOFTWARETYR B:51 , GLU B:52 , ALA B:53 , ARG C:6BINDING SITE FOR RESIDUE EDO B 148

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RPF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RPF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RPF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RPF)

(-) Exons   (0, 0)

(no "Exon" information available for 3RPF)

(-) 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:145
 aligned with MOAE_HELPY | P56422 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                             1                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139     
           MOAE_HELPY     - -MLKIIQGALDTRELLKAYQEEACAKNFGAFCVFVGIVRKEDNIQGLSFDIYEALLKTWFEKWHHKAKDLGVVLKMAHSLGDVLIGQSSFLCVSMGKNRKNALELYENFIEDFKHNAPIWKYDLIHNKRIYAKERSHPLKGSGLL 144
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh...eeeeeeee........eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee.hhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpf A   0 AVLKIIQGALDTRELLKAYQEEACAKNFGAFCVFVGIVRKEDNIQGLSFDIYEALLKTWFEKWHHKAKDLGVVLKmAHSLGDVLIGQSSFLCVSmGKNRKNALELYENFIEDFKHNAPIWKYDLIHNKRIYAKERSHPLKGSGLL 144
                                     9        19        29        39        49        59        69     |  79        89    |   99       109       119       129       139     
                                                                                                      75-MSE             94-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with MOAE_HELPY | P56422 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:146
                             1                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139      
           MOAE_HELPY     - -MLKIIQGALDTRELLKAYQEEACAKNFGAFCVFVGIVRKEDNIQGLSFDIYEALLKTWFEKWHHKAKDLGVVLKMAHSLGDVLIGQSSFLCVSMGKNRKNALELYENFIEDFKHNAPIWKYDLIHNKRIYAKERSHPLKGSGLLA 145
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MoaE-3rpfB01 B:2-116                                                                                               ----------------------------- Pfam domains (1)
           Pfam domains (2) --MoaE-3rpfB02 B:2-116                                                                                               ----------------------------- Pfam domains (2)
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh...eeeeeeee......eeeeeeeehhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpf B   0 AVLKIIQGALDTRELLKAYQEEACAKNFGAFCVFVGIVRKEDNIQGLSFDIYEALLKTWFEKWHHKAKDLGVVLKmAHSLGDVLIGQSSFLCVSmGKNRKNALELYENFIEDFKHNAPIWKYDLIHNKRIYAKERSHPLKGSGLLA 145
                                     9        19        29        39        49        59        69     |  79        89    |   99       109       119       129       139      
                                                                                                      75-MSE             94-MSE                                               


Chain C from PDB  Type:PROTEIN  Length:74
 aligned with O25482_HELPY | O25482 from UniProtKB/TrEMBL  Length:74

    Alignment length:74
                                    10        20        30        40        50        60        70    
         O25482_HELPY     1 MMVEVRFFGPIKEENFFIKANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDNLNTPLKDGDVISLLPPVCGG  74
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeee..hhhhhhhhhhh...........eeee...ee...........eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 3rpf C   1 mmVEVRFFGPIKEENFFIKANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDNLNTPLKDGDVISLLPPVCGG  74
                            ||      10        20        30        40        50        60        70    
                            1-MSE                                                                     
                             2-MSE                                                                    


Chain D from PDB  Type:PROTEIN  Length:63
 aligned with O25482_HELPY | O25482 from UniProtKB/TrEMBL  Length:74

    Alignment length:72
                                    12        22        32        42        52        62        72  
         O25482_HELPY     3 VEVRFFGPIKEENFFIKANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDNLNTPLKDGDVISLLPPVCGG  74
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --ThiS-3rpfD01 D     :5-74                                               Pfam domains (1)
           Pfam domains (2) --ThiS-3rpfD02 D     :5-74                                               Pfam domains (2)
         Sec.struct. author .eeee...........-----..hhhhhhhhhhhh......eeee...ee.----......eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3rpf D   3 VEVRFFGPIKEENFFI-----KELRAILQEKEGLKEWLGVCAIALNDHLID----PLKDGDVISLLPPVCGG  74
                                    12     |   - |      32        42        52|    |  62        72  
                                          18    24                           53   58
   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  (0, 0)

(no "SCOP Domain" information available for 3RPF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RPF)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (4, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MOAE_HELPY | P56422)
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.

Chain C,D   (O25482_HELPY | O25482)
molecular function
    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).

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