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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROKARYOTIC DOMAIN OF UNKNOWN FUNCTION (DUF849) WITH A TIM BARREL FOLD (BXE_C0966) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.75 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Aug 08  (Deposition) - 26 Aug 08  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Prokaryotic Domain Of Unknown Function (Duf849) With A Tim Barrel Fold (Yp_556190. 1) From Burkholderia Xenovorans Lb400 At 1. 75 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN DUF849 WITH A TIM BARREL FOLD
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_556190.1, BXENO_C0912, BXE_C0966
    Organism Scientific: BURKHOLDERIA XENOVORANS LB400
    Organism Taxid: 266265

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 50)

Asymmetric/Biological Unit (5, 50)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ETX7Ligand/Ion2-ETHOXYETHANOL
3IMD5Ligand/IonIMIDAZOLE
4MSE32Mod. Amino AcidSELENOMETHIONINE
5ZN4Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:49 , HIS A:51 , GLU A:258 , HOH A:502 , HOH A:503 , HOH A:504BINDING SITE FOR RESIDUE ZN A 500
02AC2SOFTWAREARG A:217 , GLY A:225 , TYR A:228 , TRP A:230 , GLN A:249 , HOH A:525BINDING SITE FOR RESIDUE ETX A 501
03AC3SOFTWAREHIS B:49 , HIS B:51 , GLU B:258 , HOH B:506 , HOH B:507 , HOH B:508BINDING SITE FOR RESIDUE ZN B 500
04AC4SOFTWAREARG B:217 , GLY B:225 , TYR B:228 , TRP B:230 , GLN B:249 , HOH B:551BINDING SITE FOR RESIDUE ETX B 501
05AC5SOFTWAREHOH A:623 , SER B:4 , VAL B:229 , MSE B:299 , HOH B:571 , HOH B:631BINDING SITE FOR RESIDUE ETX B 502
06AC6SOFTWAREGLU B:69 , ARG B:73 , ARG D:73 , SER D:76 , ASN D:77BINDING SITE FOR RESIDUE ETX B 503
07AC7SOFTWAREGLY B:163 , ASN B:164 , HOH B:609 , GLU D:129 , HOH D:758BINDING SITE FOR RESIDUE ACT B 504
08AC8SOFTWARETYR A:179 , GLY B:201 , LEU B:202 , ILE B:206 , GLY B:207BINDING SITE FOR RESIDUE IMD B 505
09AC9SOFTWAREHIS C:49 , HIS C:51 , GLU C:258 , HOH C:506 , HOH C:507 , HOH C:748BINDING SITE FOR RESIDUE ZN C 500
10BC1SOFTWAREARG C:217 , GLY C:225 , TYR C:228 , TRP C:230 , GLN C:249 , HOH C:579 , HOH C:753BINDING SITE FOR RESIDUE ETX C 501
11BC2SOFTWAREASP C:221 , ARG C:222 , PHE C:224 , GLY C:225 , ASP C:227BINDING SITE FOR RESIDUE ETX C 502
12BC3SOFTWAREARG C:237 , TRP C:262 , ALA C:264 , PRO C:265 , GLY C:266BINDING SITE FOR RESIDUE ETX C 503
13BC4SOFTWAREGLU C:95 , ARG C:99 , HOH C:701BINDING SITE FOR RESIDUE ACT C 504
14BC5SOFTWAREGLY C:201 , LEU C:202 , GLY C:205 , GLY C:207 , HOH C:744 , TYR D:179BINDING SITE FOR RESIDUE IMD C 505
15BC6SOFTWAREHIS D:49 , HIS D:51 , GLU D:258 , HOH D:504 , HOH D:505 , HOH D:506BINDING SITE FOR RESIDUE ZN D 500
16BC7SOFTWAREARG D:217 , ASP D:221 , TYR D:228 , TRP D:230 , GLN D:249 , GLY D:250 , HOH D:759BINDING SITE FOR RESIDUE IMD D 501
17BC8SOFTWARETYR C:179 , GLY D:201 , LEU D:202 , GLY D:205 , GLY D:207 , HOH D:507 , HOH D:609 , HOH D:755BINDING SITE FOR RESIDUE IMD D 502
18BC9SOFTWAREARG D:237 , TRP D:262 , ALA D:264 , PRO D:265BINDING SITE FOR RESIDUE IMD D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E49)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:192 -Pro A:193
2Pro B:192 -Pro B:193
3Pro C:192 -Pro C:193
4Pro D:192 -Pro D:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E49)

(-) Exons   (0, 0)

(no "Exon" information available for 3E49)

(-) 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:307
 aligned with Q13GE9_PARXL | Q13GE9 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q13GE9_PARXL     4 SRKVIITCAVTGAIHTPSMSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHMTVEERLRPATHYMPELASLNMGSMNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHMRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTMLGLKGPQNVNF 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......hhhhh.....hhhhhhhhhhhhhhhh..eeee.ee......ee.hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhh..eeeee...ee..hhhhhhh.....hhhhhhhhhhhhh.ee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e49 A   4 SRKVIITCAVTGAIHTPSmSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHmTVEERLRPATHYmPELASLNmGSmNFGLYPmLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHmRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTmLGLKGPQNVNF 310
                                    13        23        33        43        53        63        73        83        93       103 |     113  |    123       133       143       153       163       173       183       193       203       213  |    223       233       243       253       263       273       283       293     | 303       
                                             22-MSE                                                                92-MSE      105-MSE 113-MSE     |                                                                                          216-MSE                                                                            299-MSE       
                                                                                                                                          116-MSE  |                                                                                                                                                                                           
                                                                                                                                                 123-MSE                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with Q13GE9_PARXL | Q13GE9 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q13GE9_PARXL     4 SRKVIITCAVTGAIHTPSMSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHMTVEERLRPATHYMPELASLNMGSMNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHMRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTMLGLKGPQNVNF 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......hhhhh.....hhhhhhhhhhhhhhhh..eeee.ee......ee.hhhhhhhhhhhhhhhh..eeeee............hhhhhhhh..eeeee...ee..hhhhhhh.....hhhhhhhhhhh...ee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e49 B   4 SRKVIITCAVTGAIHTPSmSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHmTVEERLRPATHYmPELASLNmGSmNFGLYPmLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHmRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTmLGLKGPQNVNF 310
                                    13        23        33        43        53        63        73        83        93       103 |     113  |    123       133       143       153       163       173       183       193       203       213  |    223       233       243       253       263       273       283       293     | 303       
                                             22-MSE                                                                92-MSE      105-MSE 113-MSE     |                                                                                          216-MSE                                                                            299-MSE       
                                                                                                                                          116-MSE  |                                                                                                                                                                                           
                                                                                                                                                 123-MSE                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:307
 aligned with Q13GE9_PARXL | Q13GE9 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q13GE9_PARXL     4 SRKVIITCAVTGAIHTPSMSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHMTVEERLRPATHYMPELASLNMGSMNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHMRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTMLGLKGPQNVNF 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.eeee......hhhhh.....hhhhhhhhhhhhhhhh..eeee.ee......ee.hhhhh.hhhhhhhhhh..eeee.............hhhhhhhh..eeeee...ee..hhhhhhh.....hhhhhhhhhhh...ee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhh..ee.hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e49 C   4 SRKVIITCAVTGAIHTPSmSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHmTVEERLRPATHYmPELASLNmGSmNFGLYPmLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHmRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTmLGLKGPQNVNF 310
                                    13        23        33        43        53        63        73        83        93       103 |     113  |    123       133       143       153       163       173       183       193       203       213  |    223       233       243       253       263       273       283       293     | 303       
                                             22-MSE                                                                92-MSE      105-MSE 113-MSE     |                                                                                          216-MSE                                                                            299-MSE       
                                                                                                                                          116-MSE  |                                                                                                                                                                                           
                                                                                                                                                 123-MSE                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:307
 aligned with Q13GE9_PARXL | Q13GE9 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q13GE9_PARXL     4 SRKVIITCAVTGAIHTPSMSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHMTVEERLRPATHYMPELASLNMGSMNFGLYPMLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHMRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTMLGLKGPQNVNF 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......hhhhh.....hhhhhhhhhhhhhhhh..eeee.ee......ee.hhhhhhhhhhhhhhhh..eeee.............hhhhhhhh..eeeee...ee..hhhhhhh.....hhhhhhhhhhh...ee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e49 D   4 SRKVIITCAVTGAIHTPSmSPYLPVTPDEVAQASIGAAEAGAAVIHLHARDPRDGRPTQDPAAFAEFLPRIKSNTDAVINLTTGGSPHmTVEERLRPATHYmPELASLNmGSmNFGLYPmLERFKEFAHGWEREHLERSRDLVFKNTFADIEFILKTCGGNGTRFEFECYDTSHLYNLAHFVDRKLATPPFFVQTVFGLLGGIGPHPEDLAHmRRTADRLFGADYVWSILGAGRHQIPLASIGAAQGANVRVGLEDSLWIAPGELAETNAAQVRKIRQVIEGLSLEVASPAEARTmLGLKGPQNVNF 310
                                    13        23        33        43        53        63        73        83        93       103 |     113  |    123       133       143       153       163       173       183       193       203       213  |    223       233       243       253       263       273       283       293     | 303       
                                             22-MSE                                                                92-MSE      105-MSE 113-MSE     |                                                                                          216-MSE                                                                            299-MSE       
                                                                                                                                          116-MSE  |                                                                                                                                                                                           
                                                                                                                                                 123-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  (0, 0)

(no "SCOP Domain" information available for 3E49)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E49)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q13GE9_PARXL | Q13GE9)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019475    L-lysine catabolic process to acetate    The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetate.

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  3e49
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  Q13GE9_PARXL | Q13GE9
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