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(-) Description

Title :  ADENYLATE KINASE FROM SULFOLOBUS ACIDOCALDARIUS
 
Authors :  C. Vonrhein, G. E. Schulz
Date :  16 Jul 98  (Deposition) - 09 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Kinase, Thermophilic, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Vonrhein, H. Bonisch, G. Schafer, G. E. Schulz
The Structure Of A Trimeric Archaeal Adenylate Kinase.
J. Mol. Biol. V. 282 167 1998
PubMed-ID: 9733648  |  Reference-DOI: 10.1006/JMBI.1998.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21 (DE3)
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS ACIDOCALDARIUS
    Organism Taxid: 2285
    Synonym: ATP:AMP PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP3Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS C:14 , ASN C:36 , TYR C:37 , GLY C:38 , MET C:41 , ARG C:54 , MET C:57 , ARG C:58 , GLN C:69 , THR C:92 , HIS C:93 , ILE C:96 , GLY C:105 , ARG C:139 , HOH C:207 , HOH C:231BINDING SITE FOR RESIDUE AMP C 195
2AC2SOFTWARELYS D:14 , ASN D:36 , TYR D:37 , GLY D:38 , MET D:41 , ARG D:54 , MET D:57 , ARG D:58 , GLN D:69 , THR D:92 , HIS D:93 , ILE D:96 , GLY D:105 , HOH D:196 , HOH D:198 , HOH D:207 , HOH D:222BINDING SITE FOR RESIDUE AMP D 195
3AC3SOFTWARELYS F:14 , ASN F:36 , TYR F:37 , GLY F:38 , MET F:41 , ARG F:54 , MET F:57 , ARG F:58 , GLN F:69 , THR F:92 , HIS F:93 , ILE F:96 , GLY F:105 , ARG F:139 , HOH F:197 , HOH F:234 , HOH F:243BINDING SITE FOR RESIDUE AMP F 195
4AC4SOFTWAREASN C:187 , ARG C:191 , GLY F:11 , VAL F:12 , GLY F:13 , LYS F:14 , SER F:15 , THR F:16 , ARG F:132 , ARG F:135 , ASN F:177 , VAL F:178 , GLU F:179 , GLY F:180 , PRO F:182 , HOH F:240BINDING SITE FOR RESIDUE ADP F 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NKS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NKS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NKS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NKS)

(-) Exons   (0, 0)

(no "Exon" information available for 1NKS)

(-) 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:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nksa_ A: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksA00 A:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeeee..eeee..eeee...hhhhhhh...eeeeee..hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks A   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nksb_ B: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksB00 B:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhh....eeeeehhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee...eeee..eeee...hhhhhhh...eeeeee..hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks B   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain C from PDB  Type:PROTEIN  Length:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nksc_ C: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksC00 C:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeee..eeee...hhhhhhh...eeeeee..hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks C   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain D from PDB  Type:PROTEIN  Length:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nksd_ D: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksD00 D:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeee..eeee...hhhhhhh...eeeeee..hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks D   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain E from PDB  Type:PROTEIN  Length:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nkse_ E: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksE00 E:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee...eeee..eeee...hhhhhhh...eeeeee....hhh................hhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks E   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain F from PDB  Type:PROTEIN  Length:194
 aligned with KADA_SULAC | P35028 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           KADA_SULAC     1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
               SCOP domains d1nksf_ F: Adenylate kinase                                                                                                                                                                        SCOP domains
               CATH domains 1nksF00 F:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
           Pfam domains (1) ----AAA_18-1nksF01 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (1)
           Pfam domains (2) ----AAA_18-1nksF02 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (2)
           Pfam domains (3) ----AAA_18-1nksF03 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (3)
           Pfam domains (4) ----AAA_18-1nksF04 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (4)
           Pfam domains (5) ----AAA_18-1nksF05 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (5)
           Pfam domains (6) ----AAA_18-1nksF06 F:5-155                                                                                                                                 --------------------------------------- Pfam domains (6)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee..eeee..eeee...hhhhhhh...eeeeee..hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nks F   1 MKIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEARAGGEGYLFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVILETINFARYAATASAVLAGSTVKVIVNVEGDPSIAANEIIRSMK 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (KADA_SULAC | P35028)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
    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:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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