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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF PROTEIN MJ0236 (Y236_METJA)
 
Authors :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Apr 07  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Chlorine Ion, Psi-2, 10417A, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of The C-Terminal Domain Of Protein Mj0236 (Y236_metja)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0236
    Atcc: 43067
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 240-420
    Gene: MJ0236
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII DSM 2661
    Organism Taxid: 243232
    Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric/Biological Unit (2, 25)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:314 , ASN B:334 , MSE B:395 , ARG B:397BINDING SITE FOR RESIDUE CL B 1
2AC2SOFTWAREHIS A:314 , ASN A:334 , ARG A:397BINDING SITE FOR RESIDUE CL A 2
3AC3SOFTWAREHIS E:314 , ARG E:397 , HOH E:505BINDING SITE FOR RESIDUE CL E 3
4AC4SOFTWAREHIS D:314 , ARG D:397 , HOH D:484BINDING SITE FOR RESIDUE CL D 4
5AC5SOFTWAREASN B:272 , ARG B:292 , SER B:312BINDING SITE FOR RESIDUE CL B 5
6AC6SOFTWAREASN A:272 , ARG A:292 , SER A:312 , LYS B:297BINDING SITE FOR RESIDUE CL A 6
7AC7SOFTWAREHOH D:476 , ASN E:272 , ARG E:292 , SER E:312BINDING SITE FOR RESIDUE CL E 7
8AC8SOFTWARELYS A:317 , SER A:364 , THR A:365 , MSE A:366BINDING SITE FOR RESIDUE CL A 8
9AC9SOFTWARESER B:364 , THR B:365 , MSE B:366BINDING SITE FOR RESIDUE CL B 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PHP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PHP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PHP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PHP)

(-) Exons   (0, 0)

(no "Exon" information available for 2PHP)

(-) 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:181
 aligned with THIDN_METJA | Q57688 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:181
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416 
          THIDN_METJA   237 YINKEKVIKNLSYAIYLLKKMNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACMNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTMEWGTKIACEKFGGVPDIIYDRGGEGKEPMIRVLGRDAIEVVKKVEVIQKIYNTLM 417
               SCOP domains d2phpa1 A:241-420 Uncharacterized protein MJ0236                                                                                                                                    - SCOP domains
               CATH domains 2phpA00 A:241-421 L-fuculose-1-phosphate Aldolase                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh............eeee.....hhh.eeee...eee.....eee...eee..hhhhhhhhhhhhh......eeeee..hhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhh....eeee........eeeeee.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2php A 241 YINKEKVIKNLSYAIYLLKKmNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACmNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTmEWGTKIACEKFGGVPDIIYDRGGEGKEPmIRVLGRDAIEVVKKVEVIQKIYNTLE 421
                                   250       260|      270       280       290       300       310       320       330  |    340       350       360     | 370       380       390    |  400       410       420 
                                              261-MSE                                                                 333-MSE                          366-MSE                      395-MSE                      


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with THIDN_METJA | Q57688 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:186
                                                                                                                                                                                                                 417  
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413   |  
          THIDN_METJA   234 NPTYINKEKVIKNLSYAIYLLKKMNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACMNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTMEWGTKIACEKFGGVPDIIYDRGGEGKEPMIRVLGRDAIEVVKKVEVIQKIYNTLM--   -
               SCOP domains d2phpb_ B: Uncharacterized protein MJ0236                                                                                                                                                  SCOP domains
               CATH domains 2phpB00 B:238-423 L-fuculose-1-phosphate Aldolase                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh.............eeee.....hhh.eeee...eee.....eee...eee..hhhhhhhhhhhhh......eeeeee.hhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhh....eeee........eeeeee.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2php B 238 SLTYINKEKVIKNLSYAIYLLKKmNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACmNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTmEWGTKIACEKFGGVPDIIYDRGGEGKEPmIRVLGRDAIEVVKKVEVIQKIYNTLEGH 423
                                   247       257   |   267       277       287       297       307       317       327     | 337       347       357       367       377       387       397       407       417      
                                                 261-MSE                                                                 333-MSE                          366-MSE                      395-MSE                        


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with THIDN_METJA | Q57688 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:184
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413    
          THIDN_METJA   234 NPTYINKEKVIKNLSYAIYLLKKMNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACMNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTMEWGTKIACEKFGGVPDIIYDRGGEGKEPMIRVLGRDAIEVVKKVEVIQKIYNTLM 417
               SCOP domains d2phpd_ D: Uncharacterized protein MJ0236                                                                                                                                                SCOP domains
               CATH domains 2phpD00 D:238-421 L-fuculose-1-phosphate Aldolase                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh...........eeee.....hhh.eeee...eee.....eee...eee..hhhhhhhhhhhh.......eeeeee.hhhhhhhhhh...eee..........hhhhhhhhhhhhhhh....eeee........eeeeee.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2php D 238 SLTYINKEKVIKNLSYAIYLLKKmNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACmNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTmEWGTKIACEKFGGVPDIIYDRGGEGKEPmIRVLGRDAIEVVKKVEVIQKIYNTLE 421
                                   247       257   |   267       277       287       297       307       317       327     | 337       347       357       367       377       387       397       407       417    
                                                 261-MSE                                                                 333-MSE                          366-MSE                      395-MSE                      


Chain E from PDB  Type:PROTEIN  Length:183
 aligned with THIDN_METJA | Q57688 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:183
                                                                                                                                                                                                              417  
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416|  
          THIDN_METJA   237 YINKEKVIKNLSYAIYLLKKMNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACMNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTMEWGTKIACEKFGGVPDIIYDRGGEGKEPMIRVLGRDAIEVVKKVEVIQKIYNTLM--   -
               SCOP domains d2phpe_ E: Uncharacterized protein MJ0236                                                                                                                                               SCOP domains
               CATH domains 2phpE00 E:241-423 L-fuculose-1-phosphate Aldolase                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...........eeee.....hhh.eeee...eee.....eee...eee..hhhhhhhhhhhhh......eeeee..hhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhh....eeee........eeeeee.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2php E 241 YINKEKVIKNLSYAIYLLKKmNFTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKLGGFYIVGDIEFGASEHIAKIILSASKFNPEIRACmNIKYDGGLIKLLKDKFAVSSFDRKEEPPNVSTmEWGTKIACEKFGGVPDIIYDRGGEGKEPmIRVLGRDAIEVVKKVEVIQKIYNTLEGH 423
                                   250       260|      270       280       290       300       310       320       330  |    340       350       360     | 370       380       390    |  400       410       420   
                                              261-MSE                                                                 333-MSE                          366-MSE                      395-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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PHP)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D,E   (THIDN_METJA | Q57688)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008902    hydroxymethylpyrimidine kinase activity    Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
    GO:0008972    phosphomethylpyrimidine kinase activity    Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
    GO:0004789    thiamine-phosphate diphosphorylase activity    Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H(+) = diphosphate + thiamine phosphate.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

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  2php
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 Related Entries

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(-) Related Entries Specified in the PDB File

2pb9 CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF PHOSPHOMETHYLPYRIMIDINE KINASE