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(-) Description

Title :  STRUCTURE OF THE RNA LIGASE RTCB-GMP/MN(II) COMPLEX
 
Authors :  K. K. Desai, C. A. Bingman, G. N. Phillips Jr. , R. T. Raines
Date :  17 Jan 13  (Deposition) - 20 Mar 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Desai, C. A. Bingman, G. N. Phillips, R. T. Raines
Structures Of The Noncanonical Rna Ligase Rtcb Reveal The Mechanism Of Histidine Guanylylation.
Biochemistry V. 52 2518 2013
PubMed-ID: 23560983  |  Reference-DOI: 10.1021/BI4002375

(-) Compounds

Molecule 1 - TRNA-SPLICING LIGASE RTCB
    Chains: A, B
    EC Number: 6.5.1.-, 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PH1602, RTCB
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: ATCC 700860
    Synonym: PHO HYP2 INTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MN4Ligand/IonMANGANESE (II) ION
3SO419Ligand/IonSULFATE ION
4SUC2Ligand/IonSUCROSE
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SO49Ligand/IonSULFATE ION
4SUC1Ligand/IonSUCROSE
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
15GP-1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SO410Ligand/IonSULFATE ION
4SUC1Ligand/IonSUCROSE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:98 , HIS A:234 , HIS A:329 , MN A:502 , 5GP A:503BINDING SITE FOR RESIDUE MN A 501
02AC2SOFTWAREASP A:95 , CYS A:98 , ASN A:202 , HIS A:203 , MN A:501 , HOH A:841BINDING SITE FOR RESIDUE MN A 502
03AC3SOFTWAREASN A:202 , PHE A:204 , GLU A:206 , HIS A:234 , HIS A:329 , PRO A:378 , GLY A:379 , SER A:380 , MET A:381 , SER A:385 , HIS A:404 , GLY A:405 , ALA A:406 , GLY A:407 , GLU A:446 , TYR A:451 , LYS A:480 , MN A:501 , HOH A:601 , HOH A:700 , HOH A:792 , HOH A:795BINDING SITE FOR RESIDUE 5GP A 503
04AC4SOFTWARETYR A:70 , GLY A:93 , TYR A:94 , LYS A:351 , HOH A:684 , HOH A:725BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREGLY A:199 , SER A:200 , HIS A:203 , ARG A:238 , HIS A:242 , HOH A:676 , HOH A:704 , HOH A:758 , HOH A:847 , HOH A:850 , SO4 B:510BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWARELYS A:212 , ARG A:472 , HOH A:763BINDING SITE FOR RESIDUE SO4 A 506
07AC7SOFTWAREARG A:366 , ARG A:369BINDING SITE FOR RESIDUE SO4 A 507
08AC8SOFTWARESER A:184 , GLN A:185 , HOH A:786BINDING SITE FOR RESIDUE SO4 A 508
09AC9SOFTWARELYS A:342 , ARG A:343BINDING SITE FOR RESIDUE SO4 A 509
10BC1SOFTWAREARG A:425 , VAL A:435 , ARG A:436 , ALA A:437 , MET A:440 , HOH A:638 , HOH A:800 , HOH B:862BINDING SITE FOR RESIDUE SO4 A 510
11BC2SOFTWARETHR A:108 , GLU A:109 , LYS A:110 , GLY A:227 , HOH A:759 , HOH A:825 , LYS B:10 , HOH B:780BINDING SITE FOR RESIDUE SO4 A 511
12BC3SOFTWARESER A:439 , MET A:440 , ARG A:441 , HOH A:803 , ARG B:412BINDING SITE FOR RESIDUE SO4 A 512
13BC4SOFTWARELYS A:17 , ARG A:23 , PRO A:25 , TYR A:57 , LYS A:58 , ASP A:340 , HOH A:656 , HOH A:688 , HOH A:716 , HOH A:849BINDING SITE FOR RESIDUE SUC A 513
14BC5SOFTWARECYS B:98 , ASN B:202 , HIS B:234 , HIS B:329 , MN B:502 , HOH B:816BINDING SITE FOR RESIDUE MN B 501
15BC6SOFTWAREASP B:95 , CYS B:98 , HIS B:203 , MN B:501 , HOH B:740BINDING SITE FOR RESIDUE MN B 502
16BC7SOFTWAREASP B:95 , SER B:200 , HIS B:203 , ARG B:238 , HOH B:627 , HOH B:751 , HOH B:762 , HOH B:866BINDING SITE FOR RESIDUE SO4 B 503
17BC8SOFTWAREARG B:366 , ARG B:369BINDING SITE FOR RESIDUE SO4 B 504
18BC9SOFTWARELYS B:212 , ARG B:472 , HOH B:672BINDING SITE FOR RESIDUE SO4 B 505
19CC1SOFTWARESER B:411 , ARG B:412 , LYS B:413BINDING SITE FOR RESIDUE SO4 B 506
20CC2SOFTWARETYR B:70 , ILE B:74 , GLY B:93 , TYR B:94 , LYS B:351 , HOH B:743 , HOH B:875BINDING SITE FOR RESIDUE SO4 B 507
21CC3SOFTWAREARG A:257 , HOH A:651 , ARG B:23 , PRO B:54 , GLY B:55 , HOH B:606BINDING SITE FOR RESIDUE SO4 B 508
22CC4SOFTWARELYS B:258 , HOH B:778BINDING SITE FOR RESIDUE SO4 B 509
23CC5SOFTWAREARG A:190 , SO4 A:505 , HOH A:704 , SER B:439 , MET B:440 , ARG B:441 , HOH B:783 , HOH B:873BINDING SITE FOR RESIDUE SO4 B 510
24CC6SOFTWARELYS B:342 , ARG B:343BINDING SITE FOR RESIDUE SO4 B 511
25CC7SOFTWAREARG A:27 , HOH A:646 , LYS B:220 , HOH B:813 , HOH B:863BINDING SITE FOR RESIDUE SO4 B 512
26CC8SOFTWARELYS B:17 , ARG B:23 , PRO B:25 , TYR B:57 , LYS B:58 , ASP B:340 , HOH B:640 , HOH B:651 , HOH B:791BINDING SITE FOR RESIDUE SUC B 513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IT0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IT0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IT0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IT0)

(-) Exons   (0, 0)

(no "Exon" information available for 4IT0)

(-) 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:480
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4it0a_ A: Hypothetical protein PH1602                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh......eeeeeeeeeehhhhh.hhhhhhhhhhhhh................hhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhhh...eeeeeee..eeeeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4it0 A   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481


Chain B from PDB  Type:PROTEIN  Length:480
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4it0b_ B: Hypothetical protein PH1602                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..........eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeeee......eeeeeeee....eehhhhh......eeeee....hhhhhh.hhhhhhhhhhhhh................hhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........eeeeeeeeee.hhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.eeeeeeeeee..eeeeeeeeee.eee.........hhhhh....eeee.......eeeee.hhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4it0 B   2 VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG 481
                                    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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IT0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IT0)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        RTCB_PYRHO | O59245: 1uc2 4dwq 4dwr 4isj 4isz

(-) Related Entries Specified in the PDB File

4isj 4isz