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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF155 FAMILY (YP_292156.1) FROM PROCHLOROCOCCUS SP. NATL2A AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Oct 06  (Deposition) - 28 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Yp_292156. 1, Hypothetical Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Structural Genomics-Unknown Function Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Yp_292156. 1) Fro Prochlorococcus Sp. Natl2A At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_292156.1
    Organism Scientific: PROCHLOROCOCCUS MARINUS
    Organism Taxid: 59920
    Strain: NATL2A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MSE20Mod. Amino AcidSELENOMETHIONINE
4PGE3Ligand/IonTRIETHYLENE GLYCOL
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (4, 15)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , ASN A:19 , PHE A:20BINDING SITE FOR RESIDUE CL A 127
2AC2SOFTWAREGLU A:27 , THR A:28 , ARG B:88 , GLU B:102 , TYR B:104 , HOH B:147BINDING SITE FOR RESIDUE PGE B 127
3AC3SOFTWAREARG A:88 , GLU A:102 , TYR A:104 , THR B:28 , EDO B:128BINDING SITE FOR RESIDUE PGE A 128
4AC4SOFTWAREGLU C:27 , THR C:28 , ARG D:88 , GLU D:102BINDING SITE FOR RESIDUE PGE D 127
5AC5SOFTWAREARG C:88 , GLU C:102 , TYR C:104 , ARG D:10 , HOH D:141BINDING SITE FOR RESIDUE EDO C 127
6AC6SOFTWAREGLU C:68 , ASP D:62 , ASP D:64 , HOH D:187BINDING SITE FOR RESIDUE EDO C 128
7AC7SOFTWAREPGE A:128 , GLU B:27 , THR B:28 , HOH B:208 , HOH B:234BINDING SITE FOR RESIDUE EDO B 128
8AC8SOFTWARELYS D:3 , HOH D:136BINDING SITE FOR RESIDUE EDO D 128
9AC9SOFTWAREASP D:64 , ASN D:79 , GLY D:80 , ASP D:81 , ARG D:107 , HOH D:167BINDING SITE FOR RESIDUE TRS D 129

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IT9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:72 -Pro A:73
2Arg B:72 -Pro B:73
3Arg C:72 -Pro C:73
4Arg D:72 -Pro D:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IT9)

(-) Exons   (0, 0)

(no "Exon" information available for 2IT9)

(-) 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:120
 aligned with Q46J75_PROMT | Q46J75 from UniProtKB/TrEMBL  Length:126

    Alignment length:123
                             1                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119   
         Q46J75_PROMT     - -MIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVMELCDQYKLVKEQLMGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAMRSMWD 122
               SCOP domains -d2it9a1 A:1-122 Hypothetical protein PMN2A_0962                                                                            SCOP domains
               CATH domains 2it9A00 A:0-122 Transcriptional Coactivator Pc4; Chain A                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.......eeee...eeeeehhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..eeeeeeee..---....eeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it9 A   0 GmIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVmELCDQYKLVKEQLmGDEDITLELERRPWLAILNGDQYGWNLRLILSA---FNRGAEVYWPRHVTNNVVNAmRSmWD 122
                             |       9        19        29        39      | 49        59|       69        79        89   |   |99       109       119|  
                             |                                           46-MSE        60-MSE                           93  97                 117-MSE 
                             1-MSE                                                                                                                120-MSE


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q46J75_PROMT | Q46J75 from UniProtKB/TrEMBL  Length:126

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
         Q46J75_PROMT     1 MIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVMELCDQYKLVKEQLMGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAMRSM 120
               SCOP domains d2it9b_ B: Hypothetical protein PMN2A_0962                                                                               SCOP domains
               CATH domains -2it9B00 B:2-119 Transcriptional Coactivator Pc4; Chain A                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeee........eeee...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee..eeeeeeee.........eeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2it9 B   1 mIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVmELCDQYKLVKEQLmGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAmRSm 120
                            |       10        20        30        40     |  50        60        70        80        90       100       110      |120
                            |                                           46-MSE        60-MSE                                                  117-MSE
                            1-MSE                                                                                                                120-MSE


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q46J75_PROMT | Q46J75 from UniProtKB/TrEMBL  Length:126

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
         Q46J75_PROMT     1 MIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVMELCDQYKLVKEQLMGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAMRSM 120
               SCOP domains d2it9c_ C: Hypothetical protein PMN2A_0962                                                                               SCOP domains
               CATH domains -2it9C00 C:2-119 Transcriptional Coactivator Pc4; Chain A                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeee........eeee...eeeeehhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeee..eeeeeeee.........eeeeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2it9 C   1 mIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVmELCDQYKLVKEQLmGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAmRSm 120
                            |       10        20        30        40     |  50        60        70        80        90       100       110      |120
                            |                                           46-MSE        60-MSE                                                  117-MSE
                            1-MSE                                                                                                                120-MSE


Chain D from PDB  Type:PROTEIN  Length:122
 aligned with Q46J75_PROMT | Q46J75 from UniProtKB/TrEMBL  Length:126

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         Q46J75_PROMT     1 MIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVMELCDQYKLVKEQLMGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAMRSMWD 122
               SCOP domains d2it9d_ D: Hypothetical protein PMN2A_0962                                                                                 SCOP domains
               CATH domains -2it9D00 D:2-122 Transcriptional Coactivator Pc4; Chain A                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee........eeee...eeeeehhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeee..eeeeeeee.........eeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2it9 D   1 mIKKEGPGWRIIFDSSRDNFSTLIGGETWAIELDKSEWKILVEVVmELCDQYKLVKEQLmGDEDITLELERRPWLAILNGDQYGWNLRLILSASGLFNRGAEVYWPRHVTNNVVNAmRSmWD 122
                            |       10        20        30        40     |  50        60        70        80        90       100       110      |120  
                            |                                           46-MSE        60-MSE                                                  117-MSE 
                            1-MSE                                                                                                                120-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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IT9)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q46J75_PROMT | Q46J75)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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