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(-) Description

Title :  X-RAY STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET SR44
 
Authors :  A. P. Kuzin, S. Jianwei, S. Vorobiev, T. Acton, R. Xia, L. -C. Ma, G. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  24 Dec 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Northeast Structural Genomics, Sr44, X-Ray, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, S. Jianwei, S. Vorobiev, T. Acton, R. Xia, L. -C. Ma, G. Montelione, L. Tong, J. F. Hunt
X-Ray Structure Of Northeast Structural Genomics Target Sr44
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YQGN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET21
    Expression System Vector Type: VECTOR
    Gene: YQGN
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:132 , GLY A:134 , PHE A:135 , GLY A:136 , GLY A:137 , GLY A:138 , TYR A:139 , TYR A:140BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG B:132 , GLY B:134 , PHE B:135 , GLY B:136 , GLY B:137 , GLY B:138 , TYR B:139 , TYR B:140 , ASP B:141BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWAREGLY C:134 , PHE C:135 , GLY C:136 , GLY C:138 , TYR C:139 , TYR C:140 , HOH C:309BINDING SITE FOR RESIDUE SO4 C 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YDM)

(-) 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:178
 aligned with YQGN_BACSU | P54491 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
           YQGN_BACSU     4 QLRKKTLEALSALSNEDILQKTERMYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKMQFRTYQTDDQLETVYAGLLEPVIEKTKEVNPSQIDLMIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ydmA00 A:4-186 NagB/RpiA/CoA transferase-like                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhh..eeeee..---.....eee.....hhhhhhh......--.....hhhhh.eee....eee....ee........hhhhh...eeeee.hhh.ee.............eee....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydm A   4 QLRKKTLEALSALSNEDILQKTERmYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKC---TKKmQFRTYQTDDQLETVYAGLLEPV--KTKEVNPSQIDLmIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
                                    13        23    |   33        43        53        63        73 |   |  83        93       103|  |   113     | 123       133       143       153       163       173       183   
                                                   28-MSE                                         75  79  |                   104  |         119-MSE                                                               
                                                                                                         82-MSE                  107                                                                               


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with YQGN_BACSU | P54491 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
           YQGN_BACSU     4 QLRKKTLEALSALSNEDILQKTERMYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKMQFRTYQTDDQLETVYAGLLEPVIEKTKEVNPSQIDLMIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ydmB00 B:4-186 NagB/RpiA/CoA transferase-like                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhh..eeee............ee.....hhhhhhh.......-.....hhhhh.eee....eee....ee....hhhhhhhhhh..eeeee.hhh.ee.............eee....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydm B   4 QLRKKTLEALSALSNEDILQKTERmYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKmQFRTYQTDDQLETVYAGLLEPVI-KTKEVNPSQIDLmIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
                                    13        23    |   33        43        53        63        73        83        93       103 | |   113     | 123       133       143       153       163       173       183   
                                                   28-MSE                                                82-MSE                105 |         119-MSE                                                               
                                                                                                                                 107                                                                               


Chain C from PDB  Type:PROTEIN  Length:182
 aligned with YQGN_BACSU | P54491 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
           YQGN_BACSU     4 QLRKKTLEALSALSNEDILQKTERMYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKMQFRTYQTDDQLETVYAGLLEPVIEKTKEVNPSQIDLMIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ydmC00 C:4-186 NagB/RpiA/CoA transferase-like                                                                                                                                          CATH domains
           Pfam domains (1) 5-FTHF_cyc-lig-1ydmC01 C:4-179                                                                                                                                                  ------- Pfam domains (1)
           Pfam domains (2) 5-FTHF_cyc-lig-1ydmC02 C:4-179                                                                                                                                                  ------- Pfam domains (2)
           Pfam domains (3) 5-FTHF_cyc-lig-1ydmC03 C:4-179                                                                                                                                                  ------- Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhh..eeeeeee......eeeee.....hhhhhh.......-......hhhhh.eeee...eee....ee....hhhhhhhhhh....eee.hhh.ee.............eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ydm C   4 QLRKKTLEALSALSNEDILQKTERmYKYLFSLPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKmQFRTYQTDDQLETVYAGLLEPV-EKTKEVNPSQIDLmIVPGVCFDVNGFRVGFGGGYYDRYLSEYEGKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF 186
                                    13        23    |   33        43        53        63        73        83        93       103| |    113     | 123       133       143       153       163       173       183   
                                                   28-MSE                                                82-MSE               104 |          119-MSE                                                               
                                                                                                                                106
   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 1YDM)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (YQGN_BACSU | P54491)
molecular function
    GO:0030272    5-formyltetrahydrofolate cyclo-ligase activity    Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H(+) + phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.

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 Related Entries

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(-) Related Entries Specified in the PDB File

sr44
1sou