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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE AMINOTRANSFERASE (TM1131) FROM THERMOTOGA MARITIMA MSB8 AT 1.82 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  08 Oct 04  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Aminotransferase, Putative (Tm1131) From Thermotoga Maritima At 1. 82 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOTRANSFERASE, PUTATIVE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1131
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 53)

Asymmetric/Biological Unit (5, 53)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FMT27Ligand/IonFORMIC ACID
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
5UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:105 , SER A:106 , GLN A:107 , TYR A:131 , VAL A:182 , ASN A:187 , ASP A:215 , PRO A:217 , TYR A:218 , THR A:245 , SER A:247 , LYS A:248 , ARG A:255 , HOH A:641 , TYR B:69BINDING SITE FOR RESIDUE PLP A 501
02AC2SOFTWAREGLY A:39 , ASN A:187 , ARG A:381 , EDO A:604 , HOH A:667 , TYR B:69BINDING SITE FOR RESIDUE UNL A 601
03AC3SOFTWARETYR A:69 , GLY B:105 , SER B:106 , GLN B:107 , TYR B:131 , VAL B:182 , ASN B:187 , ASP B:215 , PRO B:217 , TYR B:218 , THR B:245 , SER B:247 , LYS B:248 , ARG B:255 , HOH B:673BINDING SITE FOR RESIDUE PLP B 501
04AC4SOFTWAREGLY B:38 , GLY B:39 , TYR B:131 , ASN B:187 , ARG B:381 , HOH B:743BINDING SITE FOR RESIDUE UNL B 601
05AC5SOFTWAREASP B:216 , PRO B:217 , GLY B:219 , ALA B:220 , ASN B:244 , THR B:245BINDING SITE FOR RESIDUE EDO B 602
06AC6SOFTWAREARG A:290 , GLU A:293 , ARG A:294 , HOH A:699BINDING SITE FOR RESIDUE EDO A 602
07AC7SOFTWARETHR A:93 , GLY A:94 , LEU A:95 , HOH A:646BINDING SITE FOR RESIDUE EDO A 603
08AC8SOFTWAREFMT A:617 , ASP B:119 , ASP B:120 , TYR B:141 , LEU B:142 , HOH B:672BINDING SITE FOR RESIDUE EDO B 603
09AC9SOFTWAREILE A:21 , LEU A:25 , GLY A:37 , GLY A:38 , GLY A:39 , UNL A:601 , HOH A:667BINDING SITE FOR RESIDUE EDO A 604
10BC1SOFTWARETHR B:93 , GLY B:94 , LEU B:95 , HOH B:651BINDING SITE FOR RESIDUE EDO B 604
11BC2SOFTWARELYS A:330 , TRP A:331BINDING SITE FOR RESIDUE FMT A 605
12BC3SOFTWAREASP A:216 , PRO A:217 , GLY A:219 , ALA A:220 , ASN A:244 , THR A:245BINDING SITE FOR RESIDUE FMT A 606
13BC4SOFTWAREALA A:28 , SER A:35 , GLY A:38 , LEU A:386 , HOH A:685BINDING SITE FOR RESIDUE FMT A 607
14BC5SOFTWARETHR B:45 , VAL B:249 , THR B:304 , FMT B:608BINDING SITE FOR RESIDUE FMT B 605
15BC6SOFTWAREASP A:152 , VAL A:191 , THR A:192 , HOH A:640BINDING SITE FOR RESIDUE FMT A 608
16BC7SOFTWAREILE A:92 , THR A:93 , HOH A:719BINDING SITE FOR RESIDUE FMT A 609
17BC8SOFTWARETHR A:45 , VAL A:249 , THR A:304 , HOH A:665 , HOH A:677BINDING SITE FOR RESIDUE FMT A 610
18BC9SOFTWAREPRO B:237 , GLU B:238 , VAL B:240 , VAL B:241 , GLY B:261 , SER B:262 , PHE B:265BINDING SITE FOR RESIDUE FMT B 606
19CC1SOFTWAREARG A:400 , FMT A:618 , LYS B:49 , GLU B:53 , TYR B:295BINDING SITE FOR RESIDUE FMT A 611
20CC2SOFTWAREASP B:152 , VAL B:191 , THR B:192BINDING SITE FOR RESIDUE FMT B 607
21CC3SOFTWARETHR B:45 , PHE B:46 , LYS B:248 , LEU B:250 , TYR B:308 , FMT B:605BINDING SITE FOR RESIDUE FMT B 608
22CC4SOFTWAREASP B:127 , MSE B:155 , VAL B:181 , VAL B:182 , THR B:193BINDING SITE FOR RESIDUE FMT B 609
23CC5SOFTWAREASP A:128 , LYS A:371 , VAL A:372 , TYR A:373 , GLU A:375BINDING SITE FOR RESIDUE FMT A 612
24CC6SOFTWAREASP A:127 , VAL A:181 , VAL A:182 , HIS A:186 , THR A:193BINDING SITE FOR RESIDUE FMT A 613
25CC7SOFTWAREGLY A:94 , ASP A:96 , HIS A:411BINDING SITE FOR RESIDUE FMT A 614
26CC8SOFTWARELEU A:292 , GLU A:293 , TYR A:295BINDING SITE FOR RESIDUE FMT A 615
27CC9SOFTWARELEU A:150 , GLU A:151 , ASP A:152 , HOH A:701BINDING SITE FOR RESIDUE FMT A 616
28DC1SOFTWAREASP A:120 , TYR A:141 , LEU A:142 , HOH A:672 , EDO B:603BINDING SITE FOR RESIDUE FMT A 617
29DC2SOFTWAREGLU A:401 , FMT A:611 , GLU B:53BINDING SITE FOR RESIDUE FMT A 618
30DC3SOFTWAREPHE A:348BINDING SITE FOR RESIDUE FMT A 619
31DC4SOFTWARELYS A:56 , ASP A:325 , ARG A:400 , HOH A:676 , GLU B:53BINDING SITE FOR RESIDUE FMT A 620
32DC5SOFTWARETHR B:71 , GLU B:73 , GLY B:74 , LYS B:79BINDING SITE FOR RESIDUE FMT B 610
33DC6SOFTWAREGLN B:80 , ASP B:96 , GLU B:97 , HIS B:411 , HOH B:677BINDING SITE FOR RESIDUE FMT B 611
34DC7SOFTWARESER B:70 , THR B:72BINDING SITE FOR RESIDUE FMT B 612
35DC8SOFTWARESER A:18 , HOH A:809 , VAL B:270 , GLN B:274BINDING SITE FOR RESIDUE FMT A 621
36DC9SOFTWAREPRO A:237 , VAL A:240 , VAL A:241 , GLY A:261 , SER A:262BINDING SITE FOR RESIDUE FMT A 622
37EC1SOFTWARELEU B:25 , SER B:35 , LEU B:386BINDING SITE FOR RESIDUE FMT B 613

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VP4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:128 -Pro A:129
2Asn A:187 -Pro A:188
3Asp B:128 -Pro B:129
4Asn B:187 -Pro B:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VP4)

(-) Exons   (0, 0)

(no "Exon" information available for 1VP4)

(-) 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:420
 aligned with Q9X0L5_THEMA | Q9X0L5 from UniProtKB/TrEMBL  Length:413

    Alignment length:420
                                   1                                                                                                                                                                                                                                                                                                                                                                                                                            
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
         Q9X0L5_THEMA     - -------MVVNLEGKISKIGQNMKSSIIREILKFAADKDAISFGGGVPDPETFPRKELAEIAKEIIEKEYHYTLQYSTTEGDPVLKQQILKLLERMYGITGLDEDNLIFTVGSQQALDLIGKLFLDDESYCVLDDPAYLGAINAFRQYLANFVVVPLEDDGMDLNVLERKLSEFDKNGKIKQVKFIYVVSNFHNPAGVTTSLEKRKALVEIAEKYDLFIVEDDPYGALRYEGETVDPIFKIGGPERVVLLNTFSKVLAPGLRIGMVAGSKEFIRKIVQAKQSADLCSPAITHRLAARYLERYDLLEQLKPTIELYRRKRTVMLNALEEYFSDIPGVKWVKSEGGLFIWLTLPEGFDTWEMFEYAKRKKVFYVPGRVFKVYDEPSPSMRLSFCLPPDEKIVEGIKRLREVVLEYGKEKHLL 413
               SCOP domains d1vp4a_ A: Putative aminotransferase TM1131                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh....hhhhhh........ee......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhh.eeeeehhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhhhhh.hhh.eeeeeee...........hhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eeeeee.....hhhh.eeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.......eeeee.........hhhhhhhhhee.ee.hhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vp4 A  -6 IHHHHHHmVVNLEGKISKIGQNmKSSIIREILKFAADKDAISFGGGVPDPETFPRKELAEIAKEIIEKEYHYTLQYSTTEGDPVLKQQILKLLERmYGITGLDEDNLIFTVGSQQALDLIGKLFLDDESYCVLDDPAYLGAINAFRQYLANFVVVPLEDDGmDLNVLERKLSEFDKNGKIKQVKFIYVVSNFHNPAGVTTSLEKRKALVEIAEKYDLFIVEDDPYGALRYEGETVDPIFKIGGPERVVLLNTFSKVLAPGLRIGmVAGSKEFIRKIVQAKQSADLCSPAITHRLAARYLERYDLLEQLKPTIELYRRKRTVmLNALEEYFSDIPGVKWVKSEGGLFIWLTLPEGFDTWEmFEYAKRKKVFYVPGRVFKVYDEPSPSmRLSFCLPPDEKIVEGIKRLREVVLEYGKEKHLL 413
                                   | 3        13  |     23        33        43        53        63        73        83     |  93       103       113       123       133       143       153 |     163       173       183       193       203       213       223       233       243       253    |  263       273       283       293       303       313 |     323       333       343       353       363       373      |383       393       403       413
                                   1-MSE         16-MSE                                                                   89-MSE                                                           155-MSE                                                                                                258-MSE                                                  315-MSE                               353-MSE                    380-MSE                             


Chain B from PDB  Type:PROTEIN  Length:416
 aligned with Q9X0L5_THEMA | Q9X0L5 from UniProtKB/TrEMBL  Length:413

    Alignment length:416
                               1                                                                                                                                                                                                                                                                                                                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407      
         Q9X0L5_THEMA     - ---MVVNLEGKISKIGQNMKSSIIREILKFAADKDAISFGGGVPDPETFPRKELAEIAKEIIEKEYHYTLQYSTTEGDPVLKQQILKLLERMYGITGLDEDNLIFTVGSQQALDLIGKLFLDDESYCVLDDPAYLGAINAFRQYLANFVVVPLEDDGMDLNVLERKLSEFDKNGKIKQVKFIYVVSNFHNPAGVTTSLEKRKALVEIAEKYDLFIVEDDPYGALRYEGETVDPIFKIGGPERVVLLNTFSKVLAPGLRIGMVAGSKEFIRKIVQAKQSADLCSPAITHRLAARYLERYDLLEQLKPTIELYRRKRTVMLNALEEYFSDIPGVKWVKSEGGLFIWLTLPEGFDTWEMFEYAKRKKVFYVPGRVFKVYDEPSPSMRLSFCLPPDEKIVEGIKRLREVVLEYGKEKHLL 413
               SCOP domains d1vp4b_ B: Putative aminotransferase TM1131                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------Aminotran_1_2-1vp4B01 B:31-399                                                                                                                                                                                                                                                                                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------Aminotran_1_2-1vp4B02 B:31-399                                                                                                                                                                                                                                                                                                                                                   -------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh....hhhhhh........ee......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhh.eeeeehhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh...eeeeeeee..eehhhhhhhhhhhhhhh.hhh.eeeeee............hhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eeeeee.....hhhh.eeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.......eeeee.........hhhhhhhhhee.ee.hhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vp4 B  -2 HHHmVVNLEGKISKIGQNmKSSIIREILKFAADKDAISFGGGVPDPETFPRKELAEIAKEIIEKEYHYTLQYSTTEGDPVLKQQILKLLERmYGITGLDEDNLIFTVGSQQALDLIGKLFLDDESYCVLDDPAYLGAINAFRQYLANFVVVPLEDDGmDLNVLERKLSEFDKNGKIKQVKFIYVVSNFHNPAGVTTSLEKRKALVEIAEKYDLFIVEDDPYGALRYEGETVDPIFKIGGPERVVLLNTFSKVLAPGLRIGmVAGSKEFIRKIVQAKQSADLCSPAITHRLAARYLERYDLLEQLKPTIELYRRKRTVmLNALEEYFSDIPGVKWVKSEGGLFIWLTLPEGFDTWEmFEYAKRKKVFYVPGRVFKVYDEPSPSmRLSFCLPPDEKIVEGIKRLREVVLEYGKEKHLL 413
                               |     7        17        27        37        47        57        67        77        87 |      97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257|      267       277       287       297       307       317       327       337       347     | 357       367       377  |    387       397       407      
                               1-MSE         16-MSE                                                                   89-MSE                                                           155-MSE                                                                                                258-MSE                                                  315-MSE                               353-MSE                    380-MSE
   Legend:   → Mismatch (orange background)
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  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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VP4)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X0L5_THEMA | Q9X0L5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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