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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE TRNA-(MS(2)IO(6)A)-HYDROXYLASE (PP_2188) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Oct 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Atth, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Trna-(Ms(2)Io(6)A)-Hydroxylas (Np_744337. 1) From Pseudomonas Putida Kt2440 At 2. 05 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA-(MS(2)IO(6)A)-HYDROXYLASE, PUTATIVE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_744337.1
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 31)

Asymmetric/Biological Unit (5, 31)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2FE4Ligand/IonFE (III) ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PER1Ligand/IonPEROXIDE ION
5UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:38 , GLU A:69 , HIS A:72 , GLU A:151 , FE A:502 , PER A:503 , HOH A:511 , HOH A:512BINDING SITE FOR RESIDUE FE A 501
02AC2SOFTWAREGLU A:69 , GLU A:122 , GLU A:151 , HIS A:154 , FE A:501 , PER A:503 , HOH A:512BINDING SITE FOR RESIDUE FE A 502
03AC3SOFTWAREGLU B:38 , GLU B:69 , HIS B:72 , GLU B:151 , FE B:502 , UNL B:503 , HOH B:514BINDING SITE FOR RESIDUE FE B 501
04AC4SOFTWAREGLU B:69 , GLU B:122 , GLU B:151 , HIS B:154 , FE B:501 , UNL B:503BINDING SITE FOR RESIDUE FE B 502
05AC5SOFTWAREGLU A:38 , GLU A:69 , GLU A:122 , GLU A:151 , FE A:501 , FE A:502BINDING SITE FOR RESIDUE PER A 503
06AC6SOFTWARECYS B:37 , GLU B:38 , ALA B:41 , GLU B:69 , GLU B:122 , GLU B:151 , FE B:501 , FE B:502 , EDO B:510 , HOH B:514BINDING SITE FOR RESIDUE UNL B 503
07AC7SOFTWARECYS B:37 , HIS B:196 , HOH B:595BINDING SITE FOR RESIDUE EDO B 504
08AC8SOFTWAREGLY B:12 , GLN B:75 , ARG B:78 , ARG B:82 , PHE B:143 , MSE B:183 , HOH B:522BINDING SITE FOR RESIDUE EDO B 505
09AC9SOFTWARELEU A:102 , ARG A:104 , ASP A:113 , CYS A:174 , HOH A:519 , HOH A:551BINDING SITE FOR RESIDUE EDO A 504
10BC1SOFTWAREASN B:36 , EDO B:513 , HOH B:531 , HOH B:567 , HOH B:620BINDING SITE FOR RESIDUE EDO B 506
11BC2SOFTWAREHIS A:55 , HOH A:531 , ALA B:169 , ARG B:173BINDING SITE FOR RESIDUE EDO A 505
12BC3SOFTWARETHR A:44 , ARG A:100 , THR A:114 , VAL A:117 , GLY A:118 , ILE A:121 , EDO A:510BINDING SITE FOR RESIDUE EDO A 506
13BC4SOFTWAREASN A:53 , PRO B:89 , HIS B:163 , ASN B:164 , GLY B:166 , ASP B:167BINDING SITE FOR RESIDUE EDO B 507
14BC5SOFTWARELEU B:102 , ARG B:104 , ASP B:113 , LEU B:177 , HOH B:546BINDING SITE FOR RESIDUE EDO B 508
15BC6SOFTWAREASP B:33 , ASN B:36 , LYS B:40 , ALA B:92 , GLY B:93 , HOH B:517BINDING SITE FOR RESIDUE EDO B 509
16BC7SOFTWARETHR B:44 , GLU B:69 , GLU B:122 , TYR B:158 , UNL B:503BINDING SITE FOR RESIDUE EDO B 510
17BC8SOFTWAREASP A:33 , ASN A:36 , CYS A:37 , ALA A:92 , GLY A:93 , HOH A:526BINDING SITE FOR RESIDUE EDO A 507
18BC9SOFTWAREGLN B:75 , PHE B:143 , GLY B:146 , MSE B:183 , GLN B:187BINDING SITE FOR RESIDUE EDO B 511
19CC1SOFTWAREGLU A:107 , ARG B:82 , ALA B:172 , GLU B:176 , ARG B:179BINDING SITE FOR RESIDUE EDO B 512
20CC2SOFTWARELYS A:35 , ASN A:36 , HIS A:73 , HOH A:532BINDING SITE FOR RESIDUE EDO A 508
21CC3SOFTWAREASP A:170 , ARG A:173 , ARG B:83BINDING SITE FOR RESIDUE EDO A 509
22CC4SOFTWAREILE A:49 , ASN A:53 , LYS B:35 , HIS B:73 , EDO B:506BINDING SITE FOR RESIDUE EDO B 513
23CC5SOFTWAREGLU A:122 , TYR A:158 , EDO A:506 , HOH A:535BINDING SITE FOR RESIDUE EDO A 510
24FEAAUTHORGLU A:38 , GLU A:69 , HIS A:72 , GLU A:122 , HIS A:154 , FE A:501 , FE A:502 , PER A:503 , HOH A:511 , HOH A:512DI-IRON METAL BINDING SITE FROM CHAIN A. A PEROXIDE ION (PER A503) WAS MODELED BRIDGING THE TWO IRON ATOMS. THE ASSIGNMENT OF THE PEROXIDE ION IS TENTATIVE AND IS BASED ON THE ENZYME FUNCTION AND THE ELECTRON DENSITY. HOWEVER, WE DON'T HAVE SPECTROSCOPIC DATA AT THIS TIME.
25FEBAUTHORGLU B:38 , GLU B:69 , HIS B:72 , GLU B:122 , GLU B:151 , HIS B:154 , FE B:501 , FE B:502 , UNL B:503 , HOH B:514DI-IRON METAL BINDING SITE FROM CHAIN B. NOTE THAT SITE FEB DIFFERS FROM SITE FEA. THE DENSITY FOR THE MODELED UNKNOWN LIAGND (UNL) DIFFERS FROM THE NCS DENSITY IN SITE FEA THAT WAS MODELED AS A PEROXIDE ION.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:107 -Pro A:108
2Glu B:107 -Pro B:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ITB)

(-) 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:199
 aligned with Q88KV1_PSEPK | Q88KV1 from UniProtKB/TrEMBL  Length:205

    Alignment length:199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192         
         Q88KV1_PSEPK     3 LIPEIDAFLGCPTPDAWIEAALADQETLLIDHKNCEFKAASTALSLIAKYNTHLDLINMMSRLAREELVHHEQVLRLMKRRGVPLRPVSAGRYASGLRRLVRAHEPVKLVDTLVVGAFIEARSCERFAALVPHLDEELGRFYHGLLKSEARHYQGYLKLAHNYGDEADIARCVELVRAAEMELIQSPDQELRFHSGIPQ 201
               SCOP domains d2itba1 A:3-201 Putative tRNA-(Ms(2)io(6)a)-hydroxylase PP2188                                                                                                                                          SCOP domains
               CATH domains 2itbA00 A:3-201  [code=1.20.1260.10, no name defined]                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2itb A   3 LIPEIDAFLGCPTPDAWIEAALADQETLLIDHKNCEFKAASTALSLIAKYNTHLDLINmmSRLAREELVHHEQVLRLmKRRGVPLRPVSAGRYASGLRRLVRAHEPVKLVDTLVVGAFIEARSCERFAALVPHLDEELGRFYHGLLKSEARHYQGYLKLAHNYGDEADIARCVELVRAAEmELIQSPDQELRFHSGIPQ 201
                                    12        22        32        42        52        62        72       |82        92       102       112       122       132       142       152       162       172       182|      192         
                                                                                     61-MSE             80-MSE                                                                                                183-MSE              
                                                                                      62-MSE                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with Q88KV1_PSEPK | Q88KV1 from UniProtKB/TrEMBL  Length:205

    Alignment length:198
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193        
         Q88KV1_PSEPK     4 IPEIDAFLGCPTPDAWIEAALADQETLLIDHKNCEFKAASTALSLIAKYNTHLDLINMMSRLAREELVHHEQVLRLMKRRGVPLRPVSAGRYASGLRRLVRAHEPVKLVDTLVVGAFIEARSCERFAALVPHLDEELGRFYHGLLKSEARHYQGYLKLAHNYGDEADIARCVELVRAAEMELIQSPDQELRFHSGIPQ 201
               SCOP domains d2itbb_ B: Putative tRNA-(Ms(2)io(6)a)-hydroxylase PP2188                                                                                                                                              SCOP domains
               CATH domains 2itbB00 B:4-201  [code=1.20.1260.10, no name defined]                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2itb B   4 IPEIDAFLGCPTPDAWIEAALADQETLLIDHKNCEFKAASTALSLIAKYNTHLDLINmmSRLAREELVHHEQVLRLmKRRGVPLRPVSAGRYASGLRRLVRAHEPVKLVDTLVVGAFIEARSCERFAALVPHLDEELGRFYHGLLKSEARHYQGYLKLAHNYGDEADIARCVELVRAAEmELIQSPDQELRFHSGIPQ 201
                                    13        23        33        43        53       |63        73      | 83        93       103       113       123       133       143       153       163       173       183       193        
                                                                                    61-MSE             80-MSE                                                                                                183-MSE              
                                                                                     62-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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q88KV1_PSEPK | Q88KV1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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