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(-) Description

Title :  CRYSTAL STRUCTURE OF A DUF1185 FAMILY PROTEIN (BB2672) FROM BORDETELLA BRONCHISEPTICA RB50 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  16 Jan 08  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bakolitsa, A. Kumar, K. K. Jin, D. Mcmullan, S. S. Krishna, M. D. Miller, P. Abdubek, C. Acosta, T. Astakhova, H. L. Axelrod, P. Burra, D. Carlton, C. Chen, H. J. Chiu, T. Clayton, D. Das, M. C. Deller, L. Duan, Y. Elias, K. Ellrott, D. Ernst, C. L. Farr, J. Feuerhelm, J. C. Grant, A. Grzechnik, S. K. Grzechnik, G. W. Han, L. Jaroszewski, H. A. Johnson, H. E. Klock, M. W. Knuth, P. Kozbial, D. Marciano, A. T. Morse, K. D. Murphy, E. Nigoghossian, A. Nopakun, L. Okach, J. Paulsen, C. Puckett, R. Reyes, C. L. Rife, N. Sefcovic, H. J. Tien, C. B. Trame, C. V. Trout, H. Van Den Bedem, D. Weekes, A. White, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structures Of The First Representatives Of Pfam Family Pf06684 (Duf1185) Reveal A Novel Variant Of The Bacillus Chorismate Mutase Fold And Suggest A Role In Amino-Acid Metabolism.
Acta Crystallogr. , Sect. F V. 66 1182 2010
PubMed-ID: 20944209  |  Reference-DOI: 10.1107/S1744309109050647

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN DUF1185
    Atcc: BAA-588
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_889209.1, BB2672
    Organism Scientific: BORDETELLA BRONCHISEPTICA RB50
    Organism Taxid: 257310
    Strain: RB50 / NCTC 13252

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 58)

Asymmetric Unit (4, 58)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO27Ligand/Ion1,2-ETHANEDIOL
3MSE25Mod. Amino AcidSELENOMETHIONINE
4PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (3, 108)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO54Ligand/Ion1,2-ETHANEDIOL
3MSE50Mod. Amino AcidSELENOMETHIONINE
4PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:81 , ARG A:106 , VAL A:116 , EDO A:197BINDING SITE FOR RESIDUE CL A 193
02AC2SOFTWARELYS B:81 , ARG B:106 , VAL B:116 , EDO C:202BINDING SITE FOR RESIDUE CL B 193
03AC3SOFTWAREARG B:142BINDING SITE FOR RESIDUE CL C 193
04AC4SOFTWARELYS C:81 , ARG C:106 , VAL C:116BINDING SITE FOR RESIDUE CL C 194
05AC5SOFTWAREVAL A:13 , THR A:15 , TYR A:17 , LYS A:29 , THR A:70 , EDO A:200 , HOH A:357 , HOH A:397 , ARG B:9 , GLU B:66 , HOH B:328BINDING SITE FOR RESIDUE PG4 A 194
06AC6SOFTWAREILE A:12 , GLU A:14 , GLU A:149 , HOH A:225 , ILE B:152 , GLN B:153BINDING SITE FOR RESIDUE EDO A 195
07AC7SOFTWAREGLN A:26 , LEU A:28 , ALA A:171 , HOH A:249 , HOH A:384BINDING SITE FOR RESIDUE EDO A 196
08AC8SOFTWARELYS A:81 , TRP A:103 , MSE A:115 , TYR A:140 , ARG A:142 , PHE A:145 , CL A:193BINDING SITE FOR RESIDUE EDO A 197
09AC9SOFTWAREASP A:88 , ARG A:159 , PRO B:158 , ARG B:159 , ASP C:88BINDING SITE FOR RESIDUE EDO A 198
10AD1SOFTWAREMSE B:1 , SER B:2 , LEU B:3 , ARG B:38 , THR B:181BINDING SITE FOR RESIDUE EDO B 203
11AD2SOFTWAREGLY C:21BINDING SITE FOR RESIDUE EDO C 197
12AD3SOFTWAREGLN C:26 , LEU C:28 , GLY C:170 , ALA C:171 , HOH C:224 , HOH C:234BINDING SITE FOR RESIDUE EDO C 198
13BC1SOFTWAREASN A:20 , TYR A:41 , GLY A:43 , ARG A:44 , TYR A:45 , ASP A:88 , GLY A:89 , HIS A:93 , HOH A:244 , HOH A:352BINDING SITE FOR RESIDUE EDO A 199
14BC2SOFTWAREPG4 A:194 , HOH A:287 , EDO B:200BINDING SITE FOR RESIDUE EDO A 200
15BC3SOFTWAREEDO A:202 , HOH A:312BINDING SITE FOR RESIDUE EDO A 201
16BC4SOFTWARETRP A:103 , ARG A:106 , TYR A:140 , ARG A:192 , EDO A:201BINDING SITE FOR RESIDUE EDO A 202
17BC5SOFTWAREGLN A:153 , ILE B:12 , GLU B:14 , GLU B:149 , HOH B:210 , HOH B:350BINDING SITE FOR RESIDUE EDO B 194
18BC6SOFTWARELEU B:28 , GLY B:170 , ALA B:171 , EDO B:199 , HOH B:252BINDING SITE FOR RESIDUE EDO B 195
19BC7SOFTWAREARG B:57 , TRP B:103 , SER B:107 , HOH B:230 , ARG C:44BINDING SITE FOR RESIDUE EDO B 196
20BC8SOFTWAREPRO B:22 , VAL B:173 , HIS B:174 , ALA B:175 , TYR C:45BINDING SITE FOR RESIDUE EDO B 197
21BC9SOFTWAREALA B:42 , GLY B:43 , ARG B:44 , HIS B:137 , HIS B:188 , HOH B:264 , HOH B:342BINDING SITE FOR RESIDUE EDO B 198
22CC1SOFTWAREGLN B:26 , PRO B:27 , THR B:169 , GLY B:170 , EDO B:195 , HOH B:361BINDING SITE FOR RESIDUE EDO B 199
23CC2SOFTWAREGLU A:66 , EDO A:200 , HOH A:299 , VAL B:13 , LYS B:29 , THR B:70 , EDO B:204 , HOH B:383BINDING SITE FOR RESIDUE EDO B 200
24CC3SOFTWARETYR B:140 , ARG B:192 , HOH B:374 , TRP C:103 , ARG C:106 , EDO C:201BINDING SITE FOR RESIDUE EDO B 201
25CC4SOFTWAREARG B:176 , HOH B:375 , MSE C:50BINDING SITE FOR RESIDUE EDO B 202
26CC6SOFTWAREARG A:9 , GLU A:66 , THR B:15 , LYS B:29 , EDO B:200 , HOH B:318BINDING SITE FOR RESIDUE EDO B 204
27CC7SOFTWAREARG C:9 , THR C:15 , TYR C:17 , LYS C:29 , EDO C:203 , HOH C:384BINDING SITE FOR RESIDUE PG4 C 195
28CC8SOFTWAREASN B:20 , TYR C:41 , GLY C:43 , ARG C:44 , TYR C:45 , ASP C:88 , HIS C:93 , HOH C:342 , HOH C:358BINDING SITE FOR RESIDUE EDO C 196
29DC2SOFTWAREALA A:42 , GLY A:43 , ARG A:44 , ASP C:189 , HOH C:220BINDING SITE FOR RESIDUE EDO C 199
30DC3SOFTWAREILE C:12 , GLU C:14 , GLU C:149 , ILE C:152 , GLN C:153 , HOH C:205 , HOH C:353 , HOH C:383BINDING SITE FOR RESIDUE EDO C 200
31DC4SOFTWAREEDO B:201 , TRP C:103 , ARG C:106 , SER C:107 , GLU C:111BINDING SITE FOR RESIDUE EDO C 201
32DC5SOFTWARELYS B:81 , TRP B:103 , CL B:193 , TYR C:140 , ARG C:142 , HOH C:245BINDING SITE FOR RESIDUE EDO C 202
33DC6SOFTWAREPG4 C:195 , HOH C:259BINDING SITE FOR RESIDUE EDO C 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:155 -Pro A:156
2Ala B:155 -Pro B:156
3Ala C:155 -Pro C:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BYQ)

(-) 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:191
 aligned with A0A0H3LTD0_B | A0A0H3LTD0 from UniProtKB/TrEMBL  Length:192

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         A0A0H3LTD0_B     2 SLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLMPFMAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEMEHGAVWHEAGGWAMRSVLGEPKAMVPAVKAVATAGYRMMVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVMGTGARVHARLGGLTKEAVSVHDGQR 192
               SCOP domains d3byqa1 A:2-192 Uncharacterized protein BB2672                                                                                                                                                  SCOP domains
               CATH domains 3byqA00 A:2-192 BB2672-like                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...........eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhh........eeeee......eeeeeee.....hhhhheeeee.........eeeeeeeee............hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3byq A   2 SLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLmPFmAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEmEHGAVWHEAGGWAmRSVLGEPKAmVPAVKAVATAGYRmmVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVmGTGARVHARLGGLTKEAVSVHDGQR 192
                                    11        21        31        41        51 |      61        71        81        91       101   |   111   |   121       131       141       151       161     | 171       181       191 
                                                                           50-MSE                                   91-MSE       105-MSE   115-MSE       129-MSE                               167-MSE                     
                                                                              53-MSE                                                                      130-MSE                                                          


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with A0A0H3LTD0_B | A0A0H3LTD0 from UniProtKB/TrEMBL  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
         A0A0H3LTD0_B     1 MSLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLMPFMAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEMEHGAVWHEAGGWAMRSVLGEPKAMVPAVKAVATAGYRMMVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVMGTGARVHARLGGLTKEAVSVHDGQR 192
               SCOP domains d3byqb_ B: Uncharacterized protein BB2672                                                                                                                                                        SCOP domains
               CATH domains -3byqB00 B:2-192 BB2672-like                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee...........eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhh........eeeee......eeeeeee.....hhhhheeeee.........eeeeeeeee............hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3byq B   1 mSLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLmPFmAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEmEHGAVWHEAGGWAmRSVLGEPKAmVPAVKAVATAGYRmmVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVmGTGARVHARLGGLTKEAVSVHDGQR 192
                            |       10        20        30        40        50  |     60        70        80        90|      100    |  110    |  120       130       140       150       160      |170       180       190  
                            1-MSE                                           50-MSE                                   91-MSE       105-MSE   115-MSE       129-MSE                               167-MSE                     
                                                                               53-MSE                                                                      130-MSE                                                          


Chain C from PDB  Type:PROTEIN  Length:191
 aligned with A0A0H3LTD0_B | A0A0H3LTD0 from UniProtKB/TrEMBL  Length:192

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         A0A0H3LTD0_B     2 SLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLMPFMAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEMEHGAVWHEAGGWAMRSVLGEPKAMVPAVKAVATAGYRMMVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVMGTGARVHARLGGLTKEAVSVHDGQR 192
               SCOP domains d3byqc_ C: Uncharacterized protein BB2672                                                                                                                                                       SCOP domains
               CATH domains 3byqC00 C:2-192 BB2672-like                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...........eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhh........eeeee......eeeeeee.....hhhhheeeee.........eeeeeeeee............hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3byq C   2 SLIEIRKRTLIVETTYHENGPAPAQPLKLAASCAVIRNPYAGRYEPDLmPFmAELRSLGTLLATELVDTLGKDNIEVYSKAAIVGVDGEmEHGAVWHEAGGWAmRSVLGEPKAmVPAVKAVATAGYRmmVPVHYIHASYVRSHFNSIEIGIQDAPRPREILFALVmGTGARVHARLGGLTKEAVSVHDGQR 192
                                    11        21        31        41        51 |      61        71        81        91       101   |   111   |   121       131       141       151       161     | 171       181       191 
                                                                           50-MSE                                   91-MSE       105-MSE   115-MSE       129-MSE                               167-MSE                     
                                                                              53-MSE                                                                      130-MSE
   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BYQ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BYQ)

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