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(-) Description

Title :  THE CRYSTAL STRUCTURE OF YCGJ PROTEIN FROM BACILLUS SUBITILIS AT 2.1 A RESOLUTION
 
Authors :  T. A. Burke, J. Gorman, L. Shaprio, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Nov 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, Probable Methyltransferase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Burke, J. Gorman, L. Shapiro
The Crystal Structure Of Ycgj Protein From Bacillus Subitilis At 2. 1 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YCGJ PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: MODIFIED PET 28B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YCGJ
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:-2 , HIS A:-3 , LEU A:1 , HIS A:25 , ARG A:85 , HOH A:553BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREHIS A:-3 , HIS A:-1 , HIS A:-2 , SER A:0 , TYR A:86 , TRP A:165 , LEU A:167 , HOH A:489 , HOH B:415BINDING SITE FOR RESIDUE SO4 A 404
3AC3SOFTWAREARG A:135 , ARG A:177BINDING SITE FOR RESIDUE SO4 A 406
4AC4SOFTWAREHOH A:412 , HIS B:-3 , HIS B:-1 , HIS B:-2 , SER B:0 , TYR B:86 , TRP B:165 , LEU B:167 , HOH B:424 , HOH B:511BINDING SITE FOR RESIDUE SO4 B 401
5AC5SOFTWAREHIS B:-2 , HIS B:-3 , LEU B:1 , HIS B:25 , ARG B:85 , HOH B:545BINDING SITE FOR RESIDUE SO4 B 403
6AC6SOFTWAREHIS B:-3 , ARG B:135 , ARG B:177 , HOH B:542BINDING SITE FOR RESIDUE SO4 B 405
7AC7SOFTWAREARG B:184 , GLN B:187 , ARG B:228 , HOH B:486BINDING SITE FOR RESIDUE SO4 B 407
8AC8SOFTWAREARG B:11 , PRO B:137 , ARG B:184 , HOH B:524 , HOH B:566BINDING SITE FOR RESIDUE SO4 B 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XXL)

(-) 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:234
 aligned with YCGJ_BACSU | O31474 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:234
                                                                                                                                                                                                                                                                 253  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 |  
           YCGJ_BACSU    22 EGEDLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAMFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKR--   -
               SCOP domains d1xxla_ A: Hypothetical protein YcgJ                                                                                                                                                                                                       SCOP domains
               CATH domains 1xxlA00 A:-3-230 Vaccinia Virus protein VP39                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhh......eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhh..ee.....eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xxl A  -3 HHHSLGLmIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEmVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAmFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKREG 230
                                   | 6        16        26        36        46        56        66        76        86        96       106       116       126       136       146    |  156       166       176       186       196       206       216       226    
                                   4-MSE                                    46-MSE                                                                                                  151-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with YCGJ_BACSU | O31474 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:234
                                                                                                                                                                                                                                                                 253  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 |  
           YCGJ_BACSU    22 EGEDLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAMFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKR--   -
               SCOP domains d1xxlb_ B: Hypothetical protein YcgJ                                                                                                                                                                                                       SCOP domains
               CATH domains 1xxlB00 B:-3-230 Vaccinia Virus protein VP39                                                                                                                                                                                               CATH domains
           Pfam domains (1) --------------Methyltransf_31-1xxlB01 B:11-189                                                                                                                                                   ----------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------Methyltransf_31-1xxlB02 B:11-189                                                                                                                                                   ----------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh....eeeee............eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhh..ee.....eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xxl B  -3 HHHSLGLmIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEmVEVASSFAQEKGVENVRFQQGTAESLPFPDDSFDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNHLNRLRDPSHVRESSLSEWQAmFSANQLAYQDIQKWNLPIQYDSWIKRGGTPADREKQIITHLNHASDEARDTFCITLNQNGQPISFCLKAILIQGIKREG 230
                                   | 6        16        26        36        46        56        66        76        86        96       106       116       126       136       146    |  156       166       176       186       196       206       216       226    
                                   4-MSE                                    46-MSE                                                                                                  151-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YCGJ_BACSU | O31474)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        YCGJ_BACSU | O31474: 2glu

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