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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IOLB-LIKE PROTEIN (STM4420) FROM SALMONELLA TYPHIMURIUM LT2 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jul 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Iolb-Like Protein (16422983) From Salmonella Typhimurium Lt2 At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED IOLB-LIKE PROTEIN
    Atcc: 700720
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 16422983, STM4420
    Mutation: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM LT2
    Organism Taxid: 99287
    Strain: LT2, SGSC1412

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 39)

Asymmetric Unit (6, 39)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MLY16Mod. Amino AcidN-DIMETHYL-LYSINE
4MSE6Mod. Amino AcidSELENOMETHIONINE
5NI4Ligand/IonNICKEL (II) ION
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 84)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3MLY48Mod. Amino AcidN-DIMETHYL-LYSINE
4MSE18Mod. Amino AcidSELENOMETHIONINE
5NI-1Ligand/IonNICKEL (II) ION
6SO412Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:90 , HIS A:91 , HOH A:459 , HOH A:484 , HOH A:486BINDING SITE FOR RESIDUE NI A 270
02AC2SOFTWAREHIS B:90 , HIS B:91 , HOH B:463 , HOH B:485 , HOH B:524BINDING SITE FOR RESIDUE NI B 270
03AC3SOFTWAREHIS A:170 , HIS A:172 , GLU A:185 , HIS A:228 , HOH A:296 , HOH A:297BINDING SITE FOR RESIDUE NI A 271
04AC4SOFTWAREHIS B:170 , HIS B:172 , GLU B:185 , HIS B:228 , HOH B:295 , HOH B:307BINDING SITE FOR RESIDUE NI B 271
05AC5SOFTWAREGLY A:178 , ARG A:252 , HOH A:383BINDING SITE FOR RESIDUE CL A 272
06AC6SOFTWAREARG B:70BINDING SITE FOR RESIDUE CL A 273
07AC7SOFTWAREASP B:46 , GLU B:47BINDING SITE FOR RESIDUE CL B 272
08AC8SOFTWAREARG A:130 , ARG A:137 , SER A:166BINDING SITE FOR RESIDUE CL A 274
09AC9SOFTWAREALA A:64 , ASP A:65 , SER A:66 , HOH A:308BINDING SITE FOR RESIDUE CL A 275
10BC1SOFTWAREARG B:137 , SER B:166BINDING SITE FOR RESIDUE CL B 273
11BC2SOFTWAREGLY B:178 , ARG B:252 , HOH B:386BINDING SITE FOR RESIDUE CL B 274
12BC3SOFTWAREARG A:80 , HIS A:129 , HOH A:453BINDING SITE FOR RESIDUE SO4 A 276
13BC4SOFTWAREARG B:80 , HIS B:129 , HOH B:468BINDING SITE FOR RESIDUE SO4 B 275
14BC5SOFTWAREARG A:190 , PRO A:194 , ASN A:217 , ARG A:218 , HOH A:421 , HOH A:480 , HOH A:555BINDING SITE FOR RESIDUE SO4 A 277
15BC6SOFTWAREARG B:190 , PRO B:194 , ASN B:217 , ARG B:218 , HOH B:401 , HOH B:517 , HOH B:587BINDING SITE FOR RESIDUE SO4 B 276
16BC7SOFTWARESER B:60 , PHE B:67 , MLY B:95 , THR B:97BINDING SITE FOR RESIDUE GOL B 277
17BC8SOFTWAREMLY A:62 , GLU A:93 , HOH A:536BINDING SITE FOR RESIDUE GOL A 278

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:212 -B:212

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:167 -Pro A:168
2Asn A:192 -Pro A:193
3Trp B:167 -Pro B:168
4Asn B:192 -Pro B:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QJV)

(-) 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:263
 aligned with Q8ZK62_SALTY | Q8ZK62 from UniProtKB/TrEMBL  Length:269

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
         Q8ZK62_SALTY     2 ANLLSTCTSESGNIQHISPQNAGWEYVGFDVWQLKAGESITLPSDERERCLVLVAGLASVKAADSFFYRIGQRMSPFERIPAYSVYLPHHTEAKVTAETDLELAVCSAPGFGELPVRLISPQEVGVEHRGKGRNQRLVHNILPDSQLADSLLVVEVYTNEGDTSSWPAHKHDTAVEGQETYLEETYYHRFNPPQGFCLQRVYTDDRSLDECMAVYNRDVVKVPKGYHPVATIAGYDNYYLNVMAGPLRKWRFTWEENHAWINS 264
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qjvA01    2qjvA02 A:13-125 Jelly Rolls                                                                                     2qjvA01 A:2-12,A:126-264 Jelly Rolls                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eeeeeehhhhhh....eeeeeee....eeee....eeeeeeeee..eeeee..eeeeee....hhhhh....eeee.....eeeee...eeeeeeeee.......eeehhhhheeeee.hhhhheeeeeee.........eeeeeee....ee....ee.eeee...eee.eeeeeeeee....eeeeeee......eeeeeee...eeee......eee....eeeeeeeee........ee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjv A   2 ANLLSTCTSESGNIQHISPQNAGWEYVGFDVWQLkAGESITLPSDERERCLVLVAGLASVkAADSFFYRIGQRmSPFERIPAYSVYLPHHTEAkVTAETDLELAVCSAPGFGELPVRLISPQEVGVEHRGkGRNQRLVHNILPDSQLADSLLVVEVYTNAGATSSWPAHkHDTAVEGQETYLEETYYHRFNPPQGFCLQRVYTDDRSLDECmAVYNRDVVkVPkGYHPVATIAGYDNYYLNVmAGPLRkWRFTWEENHAWINS 264
                                    11        21        31    |   41        51        61|       71   |    81        91   |   101       111       121       131|      141       151       161       171       181       191       201       211 |     221|  |   231       241  |    251       261   
                                                             36-MLY                    62-MLY       75-MSE              95-MLY                              132-MLY                                171-MLY                                   213-MSE  222-MLY               244-MSE |              
                                                                                                                                                                                                                                                         225-MLY                  250-MLY          


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q8ZK62_SALTY | Q8ZK62 from UniProtKB/TrEMBL  Length:269

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
         Q8ZK62_SALTY     2 ANLLSTCTSESGNIQHISPQNAGWEYVGFDVWQLKAGESITLPSDERERCLVLVAGLASVKAADSFFYRIGQRMSPFERIPAYSVYLPHHTEAKVTAETDLELAVCSAPGFGELPVRLISPQEVGVEHRGKGRNQRLVHNILPDSQLADSLLVVEVYTNEGDTSSWPAHKHDTAVEGQETYLEETYYHRFNPPQGFCLQRVYTDDRSLDECMAVYNRDVVKVPKGYHPVATIAGYDNYYLNVMAGPLRKWRFTWEENHAWINS 264
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qjvB01    2qjvB02 B:13-125 Jelly Rolls                                                                                     2qjvB01 B:2-12,B:126-264 Jelly Rolls                                                                                                        CATH domains
           Pfam domains (1) --KduI-2qjvB01 B:4-262                                                                                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) --KduI-2qjvB02 B:4-262                                                                                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author ...ee......eeeeeehhhhhh....eeeeeee....eeee....eeeeeeeee..eeeee..eeeeee....hhhhh...eeeee.....eeeee...eeeeeeeee.......eeehhhhheeeee.hhhhheeeeeee.........eeeeeee....ee....ee............eeeeeeeee....eeeeeee......eeeeeee...eeee......eee....eeeeeeeee........ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qjv B   2 ANLLSTCTSESGNIQHISPQNAGWEYVGFDVWQLkAGESITLPSDERERCLVLVAGLASVkAADSFFYRIGQRmSPFERIPAYSVYLPHHTEAkVTAETDLELAVCSAPGFGELPVRLISPQEVGVEHRGkGRNQRLVHNILPDSQLADSLLVVEVYTNAGATSSWPAHkHDTAVEGQETYLEETYYHRFNPPQGFCLQRVYTDDRSLDECmAVYNRDVVkVPkGYHPVATIAGYDNYYLNVmAGPLRkWRFTWEENHAWINS 264
                                    11        21        31    |   41        51        61|       71   |    81        91   |   101       111       121       131|      141       151       161       171       181       191       201       211 |     221|  |   231       241  |    251       261   
                                                             36-MLY                    62-MLY       75-MSE              95-MLY                              132-MLY                                171-MLY                                   213-MSE  222-MLY               244-MSE |              
                                                                                                                                                                                                                                                         225-MLY                  250-MLY
   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 2QJV)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZK62_SALTY | Q8ZK62)
molecular function
    GO:0008880    glucuronate isomerase activity    Catalysis of the reaction: D-glucuronate = D-fructuronate.
    GO:0016861    intramolecular oxidoreductase activity, interconverting aldoses and ketoses    Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0019310    inositol catabolic process    The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.

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  2qjv
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 Related Entries

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