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(-) Description

Title :  CBS DOMAIN PROTEIN PAE2072 FROM PYROBACULUM AEROPHILUM COMPLEXED WITH AMP
 
Authors :  T. M. Lee, N. P. King, M. R. Sawaya, D. Cascio, T. O. Yeates
Date :  10 Oct 07  (Deposition) - 17 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Cbs Domain, Bateman Domain, Amp Binding Protein, Transferase, Ligand- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. P. King, T. M. Lee, M. R. Sawaya, D. Cascio, T. O. Yeates
Structures And Functional Implications Of An Amp-Binding Cystathionine Beta-Synthase Domain Protein From A Hyperthermophilic Archaeon.
J. Mol. Biol. V. 380 181 2008
PubMed-ID: 18513746  |  Reference-DOI: 10.1016/J.JMB.2008.04.073

(-) Compounds

Molecule 1 - CONSERVED PROTEIN WITH 2 CBS DOMAINS
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: PAE2072
    Organism Scientific: PYROBACULUM AEROPHILUM
    Strain: IM2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1AMP8Ligand/IonADENOSINE MONOPHOSPHATE
2CS11Ligand/IonCESIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2CS-1Ligand/IonCESIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2CS-1Ligand/IonCESIUM ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1AMP8Ligand/IonADENOSINE MONOPHOSPHATE
2CS-1Ligand/IonCESIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:87 , HIS D:96BINDING SITE FOR RESIDUE CS B 139
02AC2SOFTWAREILE C:73 , ALA C:74 , ASN C:75BINDING SITE FOR RESIDUE CS C 139
03AC3SOFTWAREALA A:74 , ASN A:75BINDING SITE FOR RESIDUE CS A 139
04AC4SOFTWAREHIS C:96 , ASN C:97BINDING SITE FOR RESIDUE CS C 140
05AC5SOFTWAREALA B:74 , ASN B:75BINDING SITE FOR RESIDUE CS B 140
06AC6SOFTWAREARG B:95 , ASN D:75BINDING SITE FOR RESIDUE CS B 141
07AC7SOFTWAREPRO D:72 , ALA D:74BINDING SITE FOR RESIDUE CS D 139
08AC8SOFTWAREHIS B:96BINDING SITE FOR RESIDUE CS B 142
09AC9SOFTWARESER C:5 , LEU C:8BINDING SITE FOR RESIDUE CS C 141
10BC1SOFTWARESER D:5 , LEU D:8BINDING SITE FOR RESIDUE CS D 140
11BC2SOFTWAREARG A:10 , PRO A:11 , PRO A:12 , GLY A:34 , LEU A:35 , HIS A:100 , SER A:115 , ARG A:117 , ASP A:118 , ARG B:54BINDING SITE FOR RESIDUE AMP A 201
12BC3SOFTWARELEU A:35 , SER A:52 , ASP A:55 , ARG A:58 , ASN A:75 , SER A:76 , ILE A:78 , ILE A:98 , ARG A:99 , HIS A:100 , ARG D:32BINDING SITE FOR RESIDUE AMP A 301
13BC4SOFTWAREARG A:54 , ARG B:10 , PRO B:11 , PRO B:12 , GLY B:34 , LEU B:35 , HIS B:100 , SER B:115 , ARG B:117 , ASP B:118BINDING SITE FOR RESIDUE AMP B 201
14BC5SOFTWARESER B:52 , ARG B:54 , ASP B:55 , ASN B:75 , SER B:76 , PRO B:77 , ILE B:78 , ILE B:98 , ARG B:99 , HIS B:100BINDING SITE FOR RESIDUE AMP B 301
15BC6SOFTWAREARG C:10 , PRO C:11 , PRO C:12 , GLY C:34 , LEU C:35 , HIS C:100 , SER C:115 , ARG C:117 , ASP C:118 , ARG D:54BINDING SITE FOR RESIDUE AMP C 201
16BC7SOFTWAREARG B:32 , LEU C:35 , SER C:52 , ASP C:55 , ARG C:58 , ASN C:75 , SER C:76 , ILE C:78 , ILE C:98 , ARG C:99 , HIS C:100BINDING SITE FOR RESIDUE AMP C 301
17BC8SOFTWAREARG C:54 , ARG D:10 , PRO D:11 , PRO D:12 , GLY D:34 , LEU D:35 , HIS D:100 , SER D:115 , ARG D:117 , ASP D:118BINDING SITE FOR RESIDUE AMP D 201
18BC9SOFTWAREARG B:95 , ARG C:117 , SER D:52 , ARG D:54 , ASP D:55 , ASN D:75 , SER D:76 , PRO D:77 , ILE D:78 , ILE D:98 , ARG D:99 , HIS D:100BINDING SITE FOR RESIDUE AMP D 301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:120 -B:120
2C:120 -D:120

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RIF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RIF)

(-) 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:131
 aligned with Q8ZVX8_PYRAE | Q8ZVX8 from UniProtKB/TrEMBL  Length:138

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
         Q8ZVX8_PYRAE     2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELATA 132
               SCOP domains d2rifa1 A:2-132 Uncharacterized protein PAE2072                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......eee...hhhhhhhhhhhhh..eeeee.......eeeeeehhhhhhhhhh.......hhhhh....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rif A   2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELATA 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q8ZVX8_PYRAE | Q8ZVX8 from UniProtKB/TrEMBL  Length:138

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q8ZVX8_PYRAE     2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELA 130
               SCOP domains d2rifb_ B: Uncharacterized protein PAE2072                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....eee...hhhhhhhhhhhhh..eeeee.......eeeeeehhhhhhhhhh.......hhhhh....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rif B   2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELA 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with Q8ZVX8_PYRAE | Q8ZVX8 from UniProtKB/TrEMBL  Length:138

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
         Q8ZVX8_PYRAE     2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLEL 129
               SCOP domains d2rifc_ C: Uncharacterized protein PAE2072                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......eee...hhhhhhhhhhhhh..eeeee.......eeeeeehhhhhhhhhh.......hhhhh....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rif C   2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLEL 129
                                    11        21        31        41        51        61        71        81        91       101       111       121        


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with Q8ZVX8_PYRAE | Q8ZVX8 from UniProtKB/TrEMBL  Length:138

    Alignment length:130
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
         Q8ZVX8_PYRAE     2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELAT 131
               SCOP domains d2rifd_ D: Uncharacterized protein PAE2072                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------CBS-2rifD01 D:70-124                                   ------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------CBS-2rifD02 D:70-124                                   ------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------CBS-2rifD03 D:70-124                                   ------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------CBS-2rifD04 D:70-124                                   ------- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------CBS-2rifD05 D:70-124                                   ------- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------CBS-2rifD06 D:70-124                                   ------- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------CBS-2rifD07 D:70-124                                   ------- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------CBS-2rifD08 D:70-124                                   ------- Pfam domains (8)
         Sec.struct. author .hhhhh......eee...hhhhhhhhhhhhh..eeeee.......eeeeeehhhhhhhhhh.......hhhhh....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rif D   2 IRTSELLKRPPVSLPETATIREVATELAKNRVGLAVLTARDNPKRPVAVVSERDILRAVAQRLDLDGPAMPIANSPITVLDTDPVHVAAEKMRRHNIRHVVVVNKNGELVGVLSIRDLCFERAILLELAT 131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RIF)

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: CBS] (51)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8ZVX8_PYRAE | Q8ZVX8)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  2rif
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q8ZVX8_PYRAE | Q8ZVX8: 2rih

(-) Related Entries Specified in the PDB File

2rih